As filed with the Securities and Exchange Commission on January 16, 2013

Registration No. 333-185124

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Amendment
No. 4

To

FORM S-1

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

Northern Tier
Energy LP

(Exact Name of Registrant as Specified in Its Charter)

Delaware

2911

80-0763623

(State or Other Jurisdiction of

Incorporation or Organization)

(Primary Standard Industrial

Classification Code Number)

(I.R.S. Employer

Identification Number)

38C Grove Street, Suite 100

Ridgefield, Connecticut 06877

(203) 244-6550

(Address, Including Zip Code, and Telephone Number, Including Area Code, of Registrants Principal Executive Offices)

Peter T. Gelfman

Vice President, General Counsel and Secretary

38C Grove Street, Suite
100

Ridgefield, Connecticut 06877

(203) 244-6550

(Name, Address, Including Zip Code, and Telephone Number,
Including Area Code, of Agent for Service)

Copies to:

Douglas E. McWilliams

Vinson & Elkins L.L.P.

1001 Fannin, Suite 2500

Houston, Texas 77002-6760

(713) 758-2222

M. Breen Haire

Baker Botts L.L.P.

910 Louisiana Street

Houston, Texas 77002

(713) 229-1234

Approximate date of commencement of proposed sale to the public: As soon as practicable after this Registration Statement becomes
effective.

If any of the securities being registered on this form are to be offered on a delayed or continuous basis pursuant
to Rule 415 under the Securities Act of 1933, check the following box. ¨

If this form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, check the following box and list the Securities Act registration statement number
of the earlier effective registration statement for the same offering. ¨

If this form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. ¨

If this form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the
Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller
reporting company. See the definitions of large accelerated filer, accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act:

Large accelerated filer

¨

Accelerated filer

¨

Non-accelerated filer

x (Do not check if a smaller reporting company)

Smaller reporting company

¨

CALCULATION OF REGISTRATION FEE

Title of Each Class of Securities to Be Registered

Amount

to be

Registered (1)

Proposed Maximum

Offering Price Per Unit (2)

Proposed Maximum AggregateOffering Price (2)

Amount of Registration

Fee (2)

Common units representing limited partner interests

10,350,000

$24.30

$251,505,000

$34,305.28(3)

(1)

Includes common units issuable upon exercise of the underwriters option to purchase additional common units.

(2)

Calculated in accordance with Rule 457(c) on the basis of high and low sales prices January 11, 2013.

(3)

A registration fee of $34,100 was previously paid based on a prior estimate of the aggregate maximum offering price.

The Registrant hereby amends this Registration Statement on such date or dates as may be necessary to delay its effective date until
the Registrant shall file a further amendment which specifically states that this Registration Statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until the Registration Statement shall become
effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

The information in this prospectus is not complete and may be changed. We may not sell these
securities until the registration statement filed with the Securities and Exchange Commission is effective. This prospectus is not an offer to sell these securities, and we are not soliciting offers to buy these securities in any state where the
offer or sale is not permitted.

Subject to Completion, dated January 16, 2013

PROSPECTUS

Northern Tier Energy LP

9,000,000 Common Units

Representing Limited Partner Interests

The securities to be offered and sold using this prospectus are currently issued and outstanding common units representing limited partner interests in us. All of the 9,000,000 common units offered by this
prospectus are being sold by Northern Tier Holdings LLC, as the selling unitholder. Northern Tier Holdings LLC owns 100% of our general partner and, giving effect to this offering, 69.9% of our common units (or 68.4% if the underwriters exercise in
full their option to purchase additional common units). We will not receive any proceeds from the sale of the common units by the selling unitholder in this offering.

Our common units are listed on the New York Stock Exchange under the symbol NTI. On January 15, 2013, the last reported sales price of our common units on the New York Stock Exchange was $25.46 per
common unit.

Investing in our common units involves risks. See Risk Factors on page 22 to read about
factors you should consider before buying our common units.

Per Common Unit

Total

Public offering price

$

$

Underwriting discount

$

$

Proceeds to the selling unitholder

$

$

To the extent that the underwriters sell more than 9,000,000 common units, the underwriters have the option to purchase up to
an additional 1,350,000 common units at the initial public offering price less the underwriting discount.

Neither the Securities and Exchange
Commission nor any state securities regulators has approved or disapproved of these securities or passed upon the accuracy or adequacy of this prospectus. Any representation to the contrary is a criminal offense.

The underwriters expect to deliver the common units on or about ,
2013.

We have not authorized anyone to provide any information or to make any representations other than those
contained in this prospectus or in any free writing prospectuses we have prepared. We take no responsibility for, and can provide no assurance as to the reliability of, any other information that others may give you. This prospectus is an offer to
sell only the common units offered hereby, but only under circumstances and in jurisdictions where it is lawful to do so. The information contained in this prospectus is current only as of its date.

This prospectus includes industry data and forecasts that we obtained from industry publications and surveys, public filings and internal company sources. Industry publications and surveys and forecasts
generally state that the information contained therein has been obtained from sources believed to be reliable, but there can be no assurance as to the accuracy or completeness of the included information. Statements as to our ranking, market
position and market estimates are based on independent industry publications, government publications, third-party forecasts and managements estimates and assumptions about our markets and our internal research. While we are not aware of any
misstatements regarding our market, industry or similar data presented herein, such data involve risks and uncertainties and are subject to change based on various factors, including those discussed under the headings Cautionary Note Regarding
Forward-Looking Statements and Risk Factors in this prospectus.

This prospectus contains certain
information regarding refinery complexity as measured by the Nelson Complexity Index, which is calculated on an annual basis by the Oil and Gas Journal. Certain data presented in this prospectus is from the Oil and Gas Journal Report dated
January 1, 2010.

Trademarks and Trade Names

We own or have rights to various trademarks, service marks and trade names that we use in connection with the
operation of our business. This prospectus may also contain trademarks, service marks and trade names of third parties, which are the property of their respective owners. Our use or display of third parties trademarks, service marks, trade
names or products in this prospectus is not intended to, and does not imply a relationship with, or endorsement or sponsorship by us. Solely for convenience, the trademarks, service marks and trade names referred to in this prospectus may appear
without the ®, TM or SM symbols, but such references are not intended to indicate, in any way, that we will not
assert, to the fullest extent under applicable law, our rights or the right of the applicable licensor to these trademarks, service marks and trade names.

This summary highlights selected information contained elsewhere in this prospectus and is qualified in its entirety by the more
detailed information and financial statements and notes thereto included elsewhere in this prospectus. Because it is abbreviated, this summary is not complete and does not contain all of the information that you should consider before investing in
our common units. You should read the entire prospectus carefully before making an investment decision, including the information presented under the headings Risk Factors, Cautionary Note Regarding Forward-Looking
Statements, and Managements Discussion and Analysis of Financial Condition and Results of Operations and the financial statements and the notes thereto included elsewhere in this prospectus. Unless otherwise indicated, the
information presented in this prospectus assumes that the underwriters option to purchase additional common units from the selling unitholder is not exercised. We have provided definitions for certain terms used in this prospectus in the
Glossary of Industry Terms Used in this Prospectus beginning on page A-1 of this prospectus.

Unless the
context otherwise requires, the terms we, us, our, Successor and Company refer to Northern Tier Energy LP and its subsidiaries. References to our general partner refer to
Northern Tier Energy GP LLC. References to Northern Tier Holdings refers to Northern Tier Holdings LLC, the owner of our general partner. References to ACON Refining refer to ACON Refining Partners, L.L.C. and certain of its
affiliates and to TPG Refining refer to TPG Refining, L.P. and certain of its affiliates. References to Marathon Oil refer to Marathon Oil Corporation, references to Marathon Petroleum refer to Marathon Petroleum
Corporation, a wholly owned subsidiary of Marathon Oil until June 30, 2011, and references to Marathon refer to Marathon Petroleum Company LP, an indirect, wholly owned subsidiary of Marathon Petroleum, and certain affiliates of
Marathon Petroleum Company LP. References to the Marathon Acquisition refer to the acquisition by us of our St. Paul Park, Minnesota refinery, a 17% interest in the Minnesota Pipe Line Company, our convenience stores and related assets
from Marathon, completed in December 2010. We refer to the assets acquired in the Marathon Acquisition as the Marathon Assets. The Marathon Acquisition is described in greater detail, including certain related transactions in
Managements Discussion and Analysis of Financial Condition and Results of OperationsComparability of Historical ResultsMarathon Acquisition.

Northern Tier Energy LP

We are an independent downstream energy limited
partnership with refining, retail and pipeline operations that serves the Petroleum Administration for Defense District II (PADD II) region of the United States. We operate our assets in two business segments: the refining business and
the retail business. For the nine months ended September 30, 2012, we had total revenues of approximately $3.4 billion, operating income of $426.8 million, net earnings of $113.1 million and Adjusted EBITDA of $577.3 million. For the year
ended December 31, 2011, we had total revenues of $4.3 billion, operating income of $422.6 million, net earnings of $28.3 million and Adjusted EBITDA of $430.7 million. For a definition, and reconciliation, of Adjusted EBITDA to net earnings,
see Summary Historical Condensed Consolidated Financial and Other Data.

Refining Business

Our refining business primarily consists of a 74,000 barrels per calendar day (bpd) (84,500 barrels per stream day) refinery
located in St. Paul Park, Minnesota. Our refinery has a Nelson complexity index of 11.5, which refers to the ability of a refinery to produce finished products based on its investment intensity and cost relative to other refineries. Our
refinerys complexity allows us to process a variety of light, heavy, sweet and sour crudes into higher value refined products.

We are one of only two refineries in Minnesota and one of four refineries in the Upper Great Plains area within the PADD II region. The PADD II region covers Illinois, Indiana, Iowa, Kansas, Kentucky,
Michigan,

Minnesota, Missouri, Nebraska, North Dakota, South Dakota, Ohio, Oklahoma, Tennessee and Wisconsin. Our strategic location allows us direct access, primarily via the Minnesota Pipeline, to what
we believe are abundant supplies of advantageously priced crude oils. Of the crude oil processed at our refinery in the nine months ended September 30, 2012 and in the year ended December 31, 2011, approximately 44% and 51%, respectively,
was Canadian crude oil and the remainder was comprised of mostly light sweet crude oil from the Bakken Shale in North Dakota. Many of these crude oils have historically priced at a discount to the U.S. benchmark West Texas Intermediate crude oil
(NYMEX WTI). Further, over the past twelve months, NYMEX WTI has traded at an additional discount relative to waterborne crude oils, such as Brent crude oil (Brent).

We expect to continue to benefit from our access to these growing crude oil supplies. By 2030, according to the Canadian Association of
Petroleum Producers (CAPP), total Canadian crude oil production is expected to grow to 6.2 million bpd from 2011 production of 3.0 million bpd. Crude oil production from the Bakken Shale in North Dakota has also increased
significantly, helping to grow crude oil production in North Dakota from approximately 98,000 bpd in 2005 to approximately 674,000 bpd as of July 2012, and is expected to continue to grow due to improvements in unconventional resource production
techniques.

Our location also allows us to distribute our refined products throughout the midwestern United States. Our
refinery produces a broad slate of refined products including gasoline, diesel, jet fuel and asphalt, which are then marketed to resellers and consumers primarily in the PADD II region. Approximately 80% and 79% of our total refinery production for
the nine months ended September 30, 2012 and the year ended December 31, 2011, respectively, was comprised of higher value, light refined products, including gasoline and distillates.

We also own various storage and transportation assets, including a light products terminal, a heavy products terminal, storage tanks,
rail loading/unloading facilities and a Mississippi river dock. Approximately 82% and 83% of our gasoline and diesel volumes for the nine months ended September 30, 2012 and the year ended December 31, 2011, respectively, were sold via our
light products terminal to our company-operated and franchised SuperAmerica branded convenience stores, Marathon branded convenience stores and other resellers. We have a contract with Marathon to supply substantially all of the gasoline and diesel
requirements for 90 independently owned and operated Marathon branded convenience stores.

Our refining business also
includes our 17% interest in the Minnesota Pipe Line Company LLC (the Minnesota Pipe Line Company), which owns and operates the Minnesota Pipeline, a 455,000 bpd crude oil pipeline system that transports crude oil (primarily from Western
Canada and North Dakota) for approximately 300 miles from the Enbridge pipeline hub at Clearbrook, Minnesota to our refinery. The Minnesota Pipeline has historically transported the majority of the crude oil used and processed in our refinery.

Retail Business

As of September 30, 2012, our retail business operated 166 convenience stores under the SuperAmerica brand and also supported 68 franchised convenience stores, which are also operated under the
SuperAmerica brand. These convenience stores are located primarily in Minnesota and Wisconsin and sell various grades of gasoline and diesel, tobacco products and immediately consumable items such as non-alcoholic beverages, beer, prepared food and
a large variety of snacks and prepackaged items. Our refinery supplied substantially all of the gasoline and diesel sold in our company-operated and franchised convenience stores for the nine months ended September 30, 2012 and the year ended
December 31, 2011.

We also own and operate SuperMoms Bakery, which prepares and distributes baked goods and other
prepared food items for sale in our company-operated and franchised convenience stores and other third party locations.

Crude oil refining is the process of separating the hydrocarbons present in crude oil for the purpose of converting them into marketable
finished, or refined, petroleum products such as gasoline, diesel, jet fuel, asphalt and other products. Refining is primarily a margin-based business where both the feedstock (primarily crude oil) and the refined products are commodities with
fluctuating prices. In order to increase profitability, it is important for a refinery to maximize the yields of high value finished products and to minimize the costs of feedstock and operating expenses.

According to the Energy Information Administration (the EIA), as of January 1, 2011, there were 137 oil refineries
operating in the United States, with the 15 smallest each having a refining capacity of 14,000 bpd or less, and the 10 largest having capacities ranging from 330,000 bpd to 560,640 bpd.

High capital costs, historical excess capacity and environmental regulatory requirements have limited the construction of new refineries
in the United States over the past 30 years. According to the EIA, domestic operating refining capacity has increased approximately 5% between January 1982 and January 2011 from 16.1 million bpd to 16.9 million bpd. Much of this increase
in capacity is generally the result of efficiency measures and moderate expansions at various refineries, known as capacity creep, but some significant expansions at existing refineries have occurred as well. During this same time
period, more than 110 generally smaller and less efficient refineries that had limited access to a wide variety of crude oils or were unable to profitably process feedstock into a marketable product mix were closed.

According to the EIA, total demand for refined products in PADD II, which is the region in which we operate, has represented
approximately 26% of total U.S. refined products demand from 2007 to 2011. Within PADD II, refined product production capacity is currently insufficient to meet demand. For example, according to the EIA, due to product supply shortfalls within PADD
II, net receipts of gasoline, distillate and jet fuel/kerosene from domestic sources outside of PADD II comprised approximately 17%, 14% and 14%, respectively, of demand for these products. Refining capacity in the PADD II region has decreased
approximately 3% between January 1982 and January 2011 from approximately 3.8 million bpd to approximately 3.6 million bpd, while more than 25 refineries in the PADD II region have ceased operations. The refined product volumes that are
necessary to satisfy the demand in excess of PADD II production are primarily sourced from domestic refineries located outside of PADD II, specifically from the U.S. Gulf Coast.

Our Business Strategy

Our primary business objective is to grow our cash
flows from operations over the long-term by executing the following business strategies:



Make Distributions Equal to the Available Cash We Generate Each Quarter. The board of directors of our general partner adopted a
policy under which distributions for each quarter will equal the amount of available cash we generate each quarter. We do not intend to maintain excess distribution coverage in order to stabilize our quarterly distributions or to otherwise reserve
cash for future distributions. In addition, our general partner has a non-economic interest and no incentive distribution rights, and, accordingly, our unitholders will receive 100% of our cash distributions. See Managements Discussion
and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesOur Distribution Policy.



Focus on Optimizing Crude Oil Supply. We are focused on optimizing our crude oil purchases for our refining operations and minimizing
our crude oil feedstock costs. Our strategic location and our refinerys complexity allow us to receive and process a variety of light, heavy, sweet and sour crude oils from Western Canada and the United States, many of which have historically
priced at a discount to the NYMEX WTI price benchmark.

Focus on Growth Opportunities. We intend to pursue opportunities to grow our business both organically and through acquisitions
within the refining, logistics and retail marketing industries.



Organic Growth Projects. We plan to continue to make investments to enhance the operating flexibility of our refinery, to improve our
crude oil sourcing advantage and to grow our retail business. We intend to pursue organic growth projects at the refinery to improve the yield of light products we produce and the efficiency of our operations, which we believe should improve
profitability. We also plan to make investments in logistics operations, including trucking, terminal and pipeline facilities, to enhance our crude oil sourcing flexibility and to reduce related crude oil purchasing and delivery costs. We also
intend to invest in the growth of our retail business with the ultimate objective of having a dedicated outlet for all of our refinerys gasoline production. We believe that this retail strategy should allow our refinery to reduce its reliance
on the wholesale market, improve the capacity utilization of our refinery and increase our profitability.



Evaluate Accretive Acquisition Opportunities. We will selectively pursue accretive acquisitions within our refining and retail
business segments, both in our existing areas of operations as well as in new geographic regions that would diversify our operating footprint. In evaluating acquisitions within the refining industry, we will consider, among other factors,
sustainable performance of the targeted assets through the refining cycle, access to advantageous sources of crude oil supplies, attractive demand and supply market fundamentals, access to distribution and logistics infrastructure, and potential
operating synergies.



Maintain Low Leverage and Significant Liquidity in Our Business. We benefit from a number of sources of liquidity that provide us
with financial flexibility during periods of volatile commodity prices, including cash on hand, our revolving credit facility, trade credit from our crude oil suppliers and other mechanisms. For example, in December 2010, we entered into a crude oil
supply and logistics agreement with J.P. Morgan Commodities Canada Corporation (JPM CCC), which was later amended and restated in March 2012, to supply our refinerys crude oil feedstock requirements, which helps reduce the amount
of working capital required in our refinery operations. We manage our operations prudently with a focus on maintaining low leverage and sufficient liquidity to meet unforeseen capital needs. On a pro forma basis for the 2020 Notes offering and
related tender offer (as described below in Recent Developments2020 Notes Offering and Tender Offer), as of September 30, 2012, we estimate that we would have had approximately $461 million of available liquidity,
comprised of $293 million of cash on hand and $168 million available for borrowing under our $300 million revolving credit facility. Our actual available liquidity may vary from our estimated amount depending on several factors, including
fluctuations in inventory and accounts receivable values as well as cash reserves. Cash for distributions to our unitholders will be funded from this cash on hand. However, sufficient liquidity will be maintained to manage our operations.
Additionally, we seek to maintain low leverage. Our ratio of total debt as of September 30, 2012 to Adjusted EBITDA for the nine months ended September 30, 2012 was 0.5 to 1, which provides us further financial and operating flexibility.



Selectively Engage in Hedging Activities to Ensure Sufficient Cash Flows to Service Our Fixed Obligations. We plan to systematically
evaluate the merits of entering into commodity derivatives contracts to hedge our refining margins with respect to a portion of our gasoline and diesel production. We may engage in these activities with the purpose of ensuring that we have
sufficient cash flows to meet our fixed cost obligations, service our outstanding debt and other liabilities, and meet our capital expenditure requirements.

Commodity derivatives contracts that we may enter into include either exchange-traded contracts in the form of futures contracts or over-the-counter contracts in the form of commodity price swaps that
reference benchmark indices.

As of September 30, 2012, approximately nine million barrels of our future
gasoline and diesel production remained hedged under commodity derivatives contracts of which four million barrels are related to 2012 production and the remainder to 2013 production. Our hedge positions for 2011 and 2012 production were established
at the time of the Marathon Acquisition, and our plan is to hedge a lesser amount of production than we hedged at the time of the acquisition. Consequently, we plan to increase our exposure to the gross refining margins that we would realize at our
refinery on an unhedged basis over time.

For the nine months ended September 30, 2012, we settled contracts covering
approximately three million barrels of our remaining 2012 gasoline and diesel production and recognized a loss of approximately $44.6 million. In addition, during the second quarter of 2012, we reset the price of our contracts for the period of July
2012 through December 2012 and recognized a loss of approximately $92 million. We used $92 million of the net proceeds from our initial public offering to settle the majority of these obligations. The remainder of these deferred losses of
approximately $45 million will be paid through the end of 2013.

Our Competitive Strengths

We have a number of competitive strengths that we believe will help us to successfully execute our business strategy:



Strategically Located Refinery with Advantageous Access to Crude Oil Supply. Our refinery is located on approximately 170 acres along
the Mississippi River in a strategically advantageous area within the PADD II region. The refinery has the ability to source a variety of crude oils, including heavy Canadian crude oils and light North Dakota crude oils, primarily via the Minnesota
Pipeline. Our refinery also has access to crude oils from Cushing, Oklahoma, the U.S. Gulf Coast and other foreign markets. The ability to source and process multiple types of crude oil enables us to capitalize on changing market conditions and, we
believe, increase our profitability. For the nine months ended September 30, 2012, 44% of the crude oil processed at the refinery was Canadian crude oil, with the remainder comprised of locally produced U.S. crude oils, mostly from the Bakken
Shale in North Dakota. Historically, we have purchased our crude oil at a discount to the NYMEX WTI as a result of our close proximity to plentiful sources of crude oil in Western Canada and North Dakota. Over the five years ended
September 30, 2012, we realized an average discount of $2.59 per barrel of crude oil purchased for our refinery when compared to the average NYMEX WTI price per barrel over the same period. More recently, the increase of the discount at which a
barrel of NYMEX WTI traded relative to Brent has allowed refineries, such as ours, that are capable of sourcing and utilizing crude oil that is priced more in line with NYMEX WTI, to realize relatively lower feedstock costs and benefit from the
higher refined product prices resulting from higher Brent prices.



Attractive Regional Refined Products Supply/Demand Dynamics. In recent years, demand for refined products in the PADD II region has
exceeded regional production, resulting in a need for imports from other regions, specifically from the U.S. Gulf Coast region. Our inland location means that foreign and coastal domestic refiners seeking to access our marketing area would incur
additional transportation costs. Over the five years ended September 30, 2012, our refinery has realized an average price premium of $2.48 per barrel for its gasoline and distillates production relative to the prices used in calculating the
U.S. Gulf Coast 3:2:1 crack spread and an average price premium of $1.85 per barrel relative to the benchmark PADD II Group 3 3:2:1 crack spread (the Group 3 3:2:1 crack spread), in each case assuming a comparable rate of two barrels of
gasoline and one barrel of distillate (see footnote 4 in Summary Historical Condensed Consolidated Financial and Other Data).

Substantial Refinery Operating Flexibility. Since 2006, approximately $233 million (including $194 million from January 2006
through November 2010 and $39 million from our inception date of June 23, 2010 through September 30, 2012) has been invested in upgrades and capital projects to modernize the St. Paul Park refinery, improve its operating flexibility,
increase its complexity and meet U.S. environmental, health and safety requirements, including revamping the gas oil hydrotreater in 2006 to allow for the production of ultra low sulfur diesel. As a result of these capital expenditures, we believe
that we will be able to comply with known prospective fuel quality requirements without incurring significant capital costs or substantially increased operating costs. In addition, we have significant redundancies in our refining assets, which
include two crude oil distillation and vacuum towers, two reformers, two sulfur recovery units and five hydrotreating units. These redundancies allow us to continue to receive and process crude oil and other feedstocks in the event a unit goes out
of service and allows for increased maintenance flexibility as a redundant unit may be used without having to shut down the entire refinery in the case of a major unit turnaround.

Our refinery has a Nelson complexity index of 11.5. Our refinerys complexity means we can process lower cost crude oils into higher
value light refined products, including transportation fuels, such as gasoline and distillates. Gasoline and distillates comprised approximately 80% and 79% of our total refinery production for the nine months ended September 30, 2012 and the
year ended December 31, 2011, respectively.



Strong Refinery Operating and Safety Track Record. Our refinery has a strong operating and safety track record as evidenced by our
high mechanical availability and low recordable incidents. This performance is due to, among other things, the periodic upgrades and maintenance performed at our refinery. Our refinery recorded mechanical availability of 96.9%, 95.8% and 96.6% for
the years ended December 31, 2009, 2010 and 2011, respectively, with an average annual mechanical availability of 96.9% from 2005 through 2011, inclusive. We measure our safety track record primarily through the use of injury frequency rates as
determined by the Occupational Safety and Health Administration (OSHA). Our refinery had OSHA Recordable Rates of 0.75, 0.23 and 0.52 during the years ended December 31, 2009, 2010 and 2011, respectively, with an average annual OSHA
Recordable Rate of 0.97 during the period from 2005 through 2011, inclusive, and an OSHA Recordable Rate of 0.92 during the nine months ended September 30, 2012.



Integrated Refining and Retail Distribution Operations. Our business is an integrated refining operation with significant storage
assets and a retail distribution network comprising, as of September 30, 2012, 166 company-operated and 68 franchised convenience stores, all of which are operated under the SuperAmerica brand. For the nine months ended September 30,
2012 and the year ended December 31, 2011, we sold 82% and 83% of our gasoline and diesel volumes, respectively, via our eight-bay bottom-loading light products terminal located at the refinery, primarily to our retail distribution network and,
to a lesser extent, other resellers. Our refinery supplied substantially all of the gasoline and diesel sold in our company-operated and franchised convenience stores during these periods. We also have a contract with Marathon to supply
substantially all of the gasoline and diesel requirements of 90 independently owned and operated Marathon branded convenience stores. In addition, we also have (i) a seven-bay heavy products terminal located on the refinery property,
(ii) rail facilities for shipping liquefied petroleum gases and asphalt and for receiving butane, isobutane, crude oil and ethanol and (iii) a barge dock on the Mississippi River used primarily for shipping vacuum residuals and slurry.



Experienced and Proven Management Team. Our management team is led by our President and Chief Executive Officer, Hank Kuchta, who has
over 30 years of industry experience and was formerly President and Chief Operating Officer of Premcor Inc. Premcor operated four refineries in the United States with approximately 750,000 bpd of refining capacity at the time of its sale to Valero
Energy Corporation in April 2005. Prior to Premcor, Mr. Kuchta served in various management positions at

Phillips 66 Company, Tosco Corporation and Exxon Corporation. Our President of refinery operations, Greg Mullins, previously worked at Marathon for over 30 years and has extensive experience in
all aspects of refinery operations and management as well as major project development and project management. Several members of our management team, including our President and Chief Executive Officer; our Vice President, Marketing; our Vice
President, Supply; our Vice President, Human Resources; and our Vice President, Chief Information Officer, have experience working together as a management team at Premcor.

Recent Developments

Management Transition

On December 21, 2012, we announced that the Chief Executive Officer of our general partner, Mario Rodriguez, had resigned and that
President and Chief Operating Officer Hank Kuchta had assumed the role of Chief Executive Officer.

Quarterly Distribution

On November 12, 2012, we announced that the board of directors of our general partner has declared a cash
distribution attributable to the period from the closing of our initial public offering through September 30, 2012 of $1.48 per unit, payable on November 29, 2012 to unitholders of record on November 21, 2012.

2020 Notes Offering and Tender Offer

On November 8, 2012, we completed a private placement of $275 million in aggregate principal amount of 7.125% senior secured notes due 2020 (the 2020 Notes). We used the net proceeds of
the offering and cash on hand of $31 million (i) to repurchase our outstanding 10.50% senior secured notes due 2017 (the 2017 Notes) that were tendered pursuant to our previously announced tender offer and (ii) to satisfy and
discharge any remaining 2017 Notes outstanding (which notes were called for redemption after the closing of the tender offer) and to pay related fees and expenses. The indenture governing the 2020 Notes (the 2020 Indenture) has
substantially the same covenants as the indenture that governed the 2017 Notes (the 2017 Indenture), except that under the 2020 Indenture we may distribute all of our available cash (as defined in the 2020 Indenture) to our unitholders
if we maintain a fixed charge coverage ratio of 1.75 to 1.

In connection with the transactions described in the preceding
paragraph, our PIK units converted into common units representing limited partner interests with the same rights and limitations as our existing common units, effective November 9, 2012.

The repurchase of the 2017 Notes resulted in an after-tax charge of approximately $48 million.

Initial Public Offering

On July 31, 2012, we closed our initial public offering of 18,687,500 common units (the initial public offering). We used the net proceeds from our initial public offering of
approximately $245 million and cash on hand of approximately $56 million to: (i) distribute approximately $124 million to Northern Tier Holdings LLC, of which approximately $92 million was used to redeem Marathons existing preferred
interest in Northern Tier Holdings LLC and $32 million was distributed to ACON Refining, TPG Refining and entities in which our President and Chief Executive Officer holds an ownership interest, (ii) pay $92 million to J. Aron &
Company, an affiliate of Goldman, Sachs & Co., related to deferred payment obligations from the early extinguishment of derivatives, (iii) pay $40 million to Marathon, which represents the cash component of a settlement agreement
Northern Tier Energy LLC entered into with Marathon in satisfaction of a contingent consideration arrangement that was part of the Marathon Acquisition, (iv) redeem $29 million of the 2017 Notes at a redemption price of 103% of the principal
amount thereof, plus accrued interest, for an estimated $31 million, and (v) pay other offering costs of approximately $15 million.

ACON Refining Partners, L.L.C. and certain of its affiliates (ACON Refining) and TPG Refining, L.P. and certain of its
affiliates (TPG Refining) indirectly control and own a substantial majority of the economic interests in Northern Tier Holdings LLC. Northern Tier Holdings LLC owns 100% of Northern Tier Energy GP LLC, our general partner, and prior to
this offering, 79.7% of our units.

ACON Investments, L.L.C., an affiliate of ACON Refining, and certain other of its
affiliates (ACON Investments) manage private equity funds. ACON Investments has executed investments in upstream and midstream oil and gas companies as well as in energy infrastructure and energy services. TPG Global LLC (together with
its affiliates, TPG), an affiliate of TPG Refining, is a leading private investment firm with approximately $51.5 billion of assets under management as of September 30, 2012. TPG has extensive global experience with investments in
the energy sector.

Our Management

We are managed and operated by the board of directors and executive officers of our general partner, which is owned by Northern Tier Holdings. Following this offering, 69.9% of our common units will be
owned by Northern Tier Holdings (or 68.4% if the underwriters exercise in full their option to purchase additional common units). Northern Tier Holdings, as the owner of our general partner, has the right to appoint all members of the board of
directors of our general partner, including the independent directors. Our unitholders are not entitled to elect our general partner or its directors or otherwise directly participate in our management or operation. For more information about the
executive officers and directors of our general partner, please read Management.

Neither our general partner
nor its affiliates receives any management fee, but we will reimburse our general partner and its affiliates for all expenses they incur and payments they make on our behalf. Our partnership agreement provides that our general partner will determine
in good faith the expenses that are allocable to us.

Our operations are conducted through, and our operating assets are owned
by, our wholly-owned subsidiary, Northern Tier Energy LLC, and its subsidiaries. All of the employees who conduct our business are employed by Northern Tier Energy LLC and its subsidiaries. Northern Tier Energy LP does not have any employees.

Conflicts of Interest and Fiduciary Duties

Our general partner has a legal duty to manage us in good faith. However, the officers and directors of our general partner also have fiduciary duties to manage our general partner in a manner beneficial
to its indirect owners, which include ACON Refining, TPG Refining and entities in which our President and Chief Executive Officer holds an ownership interest. As a result, conflicts of interest may arise in the future between us and our unitholders,
on the one hand, and our general partner and its owners, on the other hand. Our partnership agreement limits the liability and reduces the duties owed by our general partner to our unitholders. Our partnership agreement also restricts the remedies
available to our unitholders for actions that might otherwise constitute a breach of our general partners duties. By purchasing a common unit, the purchaser agrees to be bound by the terms of our partnership agreement, and each unitholder is
treated as having consented to various actions and potential conflicts of interest contemplated in the partnership agreement that might otherwise be considered a breach of fiduciary or other duties under Delaware law.

For a more detailed description of the conflicts of interest and the fiduciary duties of our general partner, see Conflicts of
Interest and Fiduciary Duties. For a description of other relationships with our affiliates, see Certain Relationships and Related Person Transactions.

The following diagram depicts our ownership and organizational structure upon the closing of this offering:

(1)

All of the common interests in Northern Tier Holdings are owned by Northern Tier Investors, LLC, a Delaware limited liability company, the sole member of which is
Northern Tier Investors LP, a Delaware limited partnership. All of the Class A Common Units in Northern Tier Investors LP are held by ACON Refining (48.75%), TPG Refining (48.75%) and entities in which Hank Kuchta has an ownership interest
(2.5%). All of the limited liability company interests in the general partner of Northern Tier Investors LP, NTI GenPar LLC, a Delaware limited liability company, are held equally by ACON Refining and TPG Refining. Marathon holds a $45 million
preferred interest in Northern Tier Holdings. See Managements Discussion and Analysis of Financial Condition and Results of OperationsComparability of Historical ResultsMarathon Acquisition And Related Transactions.

(2)

Northern Tier Energy Holdings LLC, which elected to be treated as a corporation for federal income tax purposes in connection with the closing of our initial public
offering, is a wholly owned subsidiary of Northern Tier Energy LP and holds a 0.01% membership interest in Northern Tier Energy LLC.

(3)

Includes 17% of the limited liability company interests of Minnesota Pipe Line Company, LLC and 17% of the stock of MPL Investments, Inc.

Our principal executive offices are located at 38C Grove Street, Suite 100, Ridgefield, Connecticut 06877, and our telephone number at
that address is (203) 244-6550. Our website is located at www.ntenergy.com. We expect to make our periodic reports and other information filed with or furnished to the Securities and Exchange Commission (the SEC), available
free of charge through our website as soon as reasonably practicable after those reports and other information are electronically filed with or furnished to the SEC. Information on our website or any other website is not incorporated by reference
herein and does not constitute a part of this prospectus.

The selling unitholder has granted the underwriters a 30-day option to purchase up to an aggregate of 1,350,000 additional common units.

Immediately before this offering, the selling unitholder owned 73,227,500 common units, representing an approximate 79.7% limited partner interest in us. Following this
offering, the selling unitholder will own 64,227,500 common units, or 62,877,500 common units if the underwriters exercise in full their option to purchase additional common units, representing an approximate 69.9% and 68.4% limited partner interest
in us, respectively.

Units outstanding after this offering

91,921,112 common units.

Use of proceeds

We will not receive any of the proceeds from the sale of the common units by the selling unitholder. See Use of Proceeds.

Distribution policy

On November 12, 2012, the board of directors of our general partner declared a $1.48 per common unit distribution payable to holders of record of common units as of November 21, 2012
and payable on November 29, 2012. This distribution reflected available cash (as described below) for the period from the closing of our initial public offering through September 30, 2012.

We expect within 60 days after the end of each quarter to make distributions to unitholders of record on the applicable record date.

The board of directors of our general partner adopted a policy pursuant to which distributions for each quarter will be in an amount equal to the available cash we
generate in such quarter. Distributions on our units will be in cash. Available cash for each quarter will be determined by the board of directors of our general partner following the end of such quarter. We expect that available cash for each
quarter will generally equal our cash flow from operations for the quarter, less cash needed for maintenance capital expenditures, accrued but unpaid expenses, reimbursement of expenses incurred by our general partner and its affiliates, debt
service and other contractual obligations and reserves for future operating or capital needs that the board of directors of our general partner deems necessary or appropriate, including reserves for our turnaround and related expenses.

We do not intend to maintain excess distribution coverage for the purpose of maintaining stability or growth in our quarterly

distribution or to otherwise reserve cash for distributions, and we do not intend to incur debt to pay quarterly distributions. We expect to finance substantially all of our growth externally,
either by debt issuances or additional issuances of equity.

Because our policy will be to distribute an amount equal to all available cash we generate each quarter, our unitholders will have direct exposure to fluctuations in
the amount of cash generated by our business. We expect that the amount of our quarterly distributions, if any, will vary based on our operating cash flow during such quarter. As a result, our quarterly distributions, if any, will not be stable and
will vary from quarter to quarter as a direct result of variations in, among other factors, (i) our operating performance, (ii) cash flows caused by, among other things, fluctuations in the prices of crude oil and other feedstocks and the
prices we receive for finished products, working capital or capital expenditures and (iii) cash reserves deemed necessary or appropriate by the board of directors of our general partner. Such variations in the amount of our quarterly
distributions may be significant. Unlike most publicly traded partnerships, we do not have a minimum quarterly distribution or employ structures intended to consistently maintain or increase distributions over time. The board of directors of our
general partner may change our distribution policy at any time. Our partnership agreement does not require us to pay distributions to our unitholders on a quarterly or other basis.

Incentive distribution rights

None.

Subordination period

None.

Issuance of additional units

Our partnership agreement authorizes us to issue an unlimited number of additional units, units with rights to distributions or in liquidation that are senior to our common units, and rights to
buy units for the consideration and on the terms and conditions determined by the board of directors of our general partner, without the approval of our unitholders. See Common Units Eligible for Future Sale and The Partnership
AgreementIssuance of Additional Partnership Interests.

Limited voting rights

Our general partner manages and operates us. Unlike the holders of common stock in a corporation, our unitholders will have only limited voting rights on matters affecting our business.
Unitholders will have no right to elect our general partner or our general partners directors on an annual or other continuing basis. Our general partner may be removed by a vote of the holders of at least two-thirds of the outstanding units,
including any units owned by our general partner and its affiliates (including Northern Tier Holdings). Following completion of this offering, Northern Tier Holdings will own an aggregate of approximately 69.9% of our outstanding common units (or
approximately 68.4% of our outstanding common units if the underwriters exercise their option to purchase additional common units

in full). This will give Northern Tier Holdings the ability to prevent removal of our general partner. See The Partnership AgreementVoting Rights.

Call right

If at any time our general partner and its affiliates (including Northern Tier Holdings) own more than 90% of the outstanding common units, our general partner will have the right, but not the
obligation, to purchase all, but not less than all, of the units held by unaffiliated unitholders at a price not less than their then-current market price, as calculated pursuant to the terms of our partnership agreement. See The Partnership
AgreementCall Right.

Material federal income tax consequences

For a discussion of the material federal income tax consequences that may be relevant to prospective unitholders, see Material Federal Income Tax Consequences.

Exchange listing

Our common units are listed on the New York Stock Exchange (NYSE) under the symbol NTI.

The following tables present certain summary historical condensed consolidated financial and other data. The combined financial
statements for the year ended December 31, 2009 and the eleven months ended November 30, 2010 represent a carve-out financial statement presentation of several operating units of Marathon, which we refer to as Predecessor. For
more information on the carve-out presentation, see Managements Discussion and Analysis of Financial Condition and Results of OperationsPredecessor Carve-Out Financial Statements and our financial statements and the notes
thereto included elsewhere in this prospectus. The historical combined financial data for periods prior to December 1, 2010 presented below do not reflect the consummation of the Marathon Acquisition and the transactions related thereto or our
capital structure following the Marathon Acquisition and the transactions related thereto. Northern Tier Energy LLC was formed on June 23, 2010 and entered into certain agreements with Marathon on October 6, 2010 to acquire the Marathon
Assets. At the closing of the Marathon Acquisition on December 1, 2010, Northern Tier Energy LLC acquired the Marathon Assets. Northern Tier Energy LLC had no operating activities between its inception date and the closing date of the Marathon
Acquisition, although it incurred various transaction and formation costs which have been included in the period June 23, 2010 (inception date) through December 31, 2010 (the 2010 Successor Period). Upon the closing of our
initial public offering, the historical consolidated financial statements of Northern Tier Energy LLC became the historical consolidated financial statements of Northern Tier Energy LP.

The summary historical financial data as of September 30, 2012 and for the nine months ended September 30, 2011 and 2012 are
derived from unaudited financial statements and the notes thereto included elsewhere in this prospectus. The summary historical financial data as of December 31, 2010 and 2011, for the year ended December 31, 2009, the eleven months ended
November 30, 2010, the 2010 Successor Period and the year ended December 31, 2011 are derived from audited financial statements and the notes thereto included elsewhere in this prospectus. The summary historical combined balance sheet data
as of November 30, 2010 and December 31, 2009 are derived from audited financial statements and the notes thereto and the summary historical balance sheet data as of September 30, 2011 is derived from unaudited financial statements
and the notes thereto that are not included in this prospectus.

On a pro forma basis and adjusted for certain items to give
effect to our initial public offering, the tendering of our 2017 Notes and the private placement of our 2020 Notes, net earnings for the year ended December 31, 2011 would have been $33.1 million.

The items related to our initial public offering include a reduction of interest expense of $3.0 million related to the redemption of a
portion of the 2017 Notes, increased selling, general and administrative expenses of $3.5 million as a result of being a publicly traded partnership (resulting in pro forma selling, general and administrative expense of $94.2 million for the year
ended December 31, 2011) and a reduction of $2.1 million in management fees paid to ACON Management and TPG Management (resulting in pro forma other income of $6.6 million for the year ended December 31, 2011).

As a result of the elections by Northern Tier Retail Holdings LLC, a wholly owned subsidiary of Northern Tier Energy LLC that holds all
of the ownership interests in Northern Tier Retail LLC and Northern Tier Bakery LLC, and Northern Tier Energy Holdings LLC to be treated as corporations for federal income tax purposes, for periods following such elections, our financial statements
will include a tax provision on income attributable to these subsidiaries. Giving effect to such elections, we recorded a tax provision of $7.8 million for the nine months ended September 30, 2012, including an $8.0 million tax charge to
recognize the net deferred tax asset and liability position as of the date of the elections. On a pro forma basis after giving effect to such elections and our initial public offering, we would have recorded a tax provision of approximately $5.7
million for the year ended December 31, 2011 (resulting in a pro forma income tax provision of $5.7 million for the year ended December 31, 2011).

On November 8, 2012, we completed a private placement of $275 million in aggregate
principal amount of the 2020 Notes. We used the net proceeds of the offering and cash on hand of $31 million (i) to repurchase our outstanding 2017 Notes that were tendered pursuant to our previously announced tender offer and (ii) to satisfy and
discharge any remaining 2017 Notes outstanding (which notes were called for redemption after the closing of the tender offer) and to pay related fees and expenses. The repurchase of the 2017 Notes resulted in an after-tax charge of approximately $48
million in the fourth quarter of 2012. On a pro forma basis after giving effect to such private placement and tender offer, we would have recorded a reduction of approximately $8.9 million of interest expense for the year ended December 31,
2011. The pro forma impacts of the private placement and tender offer and the pro forma impacts of the partial redemption of the 2017 Notes as part of our initial public offering would have resulted in a pro forma interest expense of $30.2 million
for the year ended December 31, 2011.

You should read the following tables along with Risk Factors, Use of
Proceeds, Capitalization, Selected Historical Condensed Consolidated Financial Data, Managements Discussion and Analysis of Financial Condition and Results of Operations, Business and our
financial statements and the notes thereto included elsewhere in this prospectus.

Total equity for the Predecessor represents a net balance reflecting Marathons investment and the effect of participation in Marathons centralized cash
management programs. All cash receipts were remitted to, and all cash disbursements were funded by, Marathon. Other transactions affecting the net investment include general, administrative and overhead costs incurred by Marathon that were allocated
to the Predecessor. There are no terms of settlement or interest charges associated with the net investment balance.

EBITDA is defined as net earnings before interest expense, income taxes and depreciation and amortization. Adjusted EBITDA is defined as EBITDA before turnaround and
related expenses, stock-based compensation expense, gains (losses) from derivative activities, contingent consideration fair value adjustments, formation costs, bargain purchase gain and adjustments to reflect proportionate EBITDA from the Minnesota
Pipeline operations. We believe Adjusted EBITDA is an important measure of operating performance and provides useful information to investors because it highlights trends in our business that may not otherwise be apparent when relying solely on GAAP
measures and because it eliminates items that have less bearing on our operating performance. We also believe Adjusted EBITDA may be used by some investors to assess the ability of our assets to generate sufficient cash flow to make distributions to
our unitholders.

Adjusted EBITDA, as presented herein, is a supplemental measure of our performance that is not
required by, or presented in accordance with, GAAP. We use non-GAAP financial measures as supplements to our GAAP results in order to provide a more complete understanding of the factors and trends affecting our business. Adjusted EBITDA is a
measure of operating performance that is not defined by GAAP and should not be considered a substitute for net (loss) earnings as determined in accordance with GAAP.

Set forth below is additional detail as to how we use Adjusted EBITDA as a measure of operating performance, as well as a discussion of the limitations of Adjusted EBITDA as an analytical tool.

Operating Performance. Management uses Adjusted EBITDA in a number of ways to assess our combined financial
and operating performance, and we believe this measure is helpful to management and investors in identifying trends in our performance. We use Adjusted EBITDA as a measure of our combined operating performance exclusive of income and expenses that
relate to the financing, derivative activities, income taxes and capital investments of the business, adjusted to reflect EBITDA from the Minnesota Pipeline operations. In addition, Adjusted EBITDA helps management identify controllable expenses and
make decisions designed to help us meet our current financial goals and optimize our financial performance. Accordingly, we believe this metric measures our financial performance based on operational factors that management can impact in the
short-term, namely the cost structure and expenses of the organization.

Limitations. Other companies,
including other companies in our industry, may calculate Adjusted EBITDA differently than we do, limiting its usefulness as a comparative measure. Adjusted EBITDA also has limitations as an analytical tool and should not be considered in isolation
or as a substitute for analysis of our results as reported under GAAP. Some of these limitations include that Adjusted EBITDA:



does not reflect our cash expenditures, or future requirements, for capital expenditures or contractual commitments;



does not reflect changes in, or cash requirements for, our working capital needs;



does not reflect our interest expense, or the cash requirements necessary to service interest or principal payments, on our debt;



does not reflect the equity income in our Minnesota Pipe Line Company investment, but includes 17% of the calculated EBITDA of Minnesota Pipe Line
Company;



does not reflect realized and unrealized gains and losses from hedging activities, which may have a substantial impact on our cash flow;



does not reflect certain other non-cash income and expenses; and



excludes income taxes that may represent a reduction in available cash.

The following table shows the reconciliation of net earnings, the most directly
comparable GAAP measure, to EBITDA and Adjusted EBITDA for the year ended December 31, 2009, the eleven months ended November 30, 2010, the 2010 Successor Period, the year ended December 31, 2011 and the nine months ended
September 30, 2011 and 2012:

Predecessor

Successor

Year EndedDecember 31,2009

Eleven MonthsEndedNovember 30,2010

June 23, 2010(inception date)to December 31,2010

Year EndedDecember 31,2011

Nine Months EndedSeptember 30,

2011

2012

(In millions)

Net earnings (loss)

$

54.7

$

61.0

$

24.8

$

28.3

$

(264.4

)

$

113.1

Adjustments:

Interest expense

0.4

0.3

3.2

42.1

30.6

36.7

Depreciation and amortization

40.2

37.3

2.2

29.5

22.3

24.6

Income tax provision

34.8

67.1







7.8

EBITDA subtotal

130.1

165.7

30.2

99.9

(211.5

)

182.2

Minnesota Pipe Line Company proportionate EBITDA

4.2

3.7

0.3

2.8

2.7

2.1

Turnaround and related expenses

0.6

9.5



22.6

22.5

17.1

Equity-based compensation expense

0.3

0.3

0.1

1.6

1.1

1.4

Unrealized losses (gains) on derivative activities



40.9

27.1

41.9

334.5

(32.6

)

Contingent consideration (income) loss







(55.8

)

(37.6

)

104.3

Formation costs





3.6

7.4

6.1

1.0

Loss on early extinguishment of derivatives











136.8

Bargain purchase gain





(51.4

)







Realized losses on derivative activities







310.3

246.4

165.0

Adjusted EBITDA

$

135.2

$

220.1

$

9.9

$

430.7

$

364.2

$

577.3

(3)

Refinery gross product margin per barrel of throughput is a per barrel measurement calculated by subtracting refinery costs of sales from total refinery revenues and
dividing the difference by the total throughput for the respective periods presented. Refinery gross product margin is a non-GAAP performance measure that we believe is important to investors in evaluating our refinery performance as a general
indication of the amount above our cost of products that we are able to sell refined products. Each of the components used in this calculation (revenues and cost of sales) can be reconciled directly to our statements of operations. Our calculation
of refinery gross product margin may differ from similar calculations of other companies in our industry, thereby limiting its usefulness as a comparative measure.

The following table shows the reconciliation of refinery gross product margin per
barrel of throughput for the year ended December 31, 2009, the eleven months ended November 30, 2010, the 2010 Successor Period, the year ended December 31, 2011 and the nine months ended September 30, 2011 and 2012:

Predecessor

Successor

Year
EndedDecember 31,2009

Eleven MonthsEndedNovember 30,2010

June 23, 2010(inception date)to December 31,2010

Year
EndedDecember 31,2011

Nine Months EndedSeptember 30,

2011

2012

(In millions, except gross margin per barrel data)

Refinery revenue

$

2,530.7

$

2,799.8

$

312.2

$

3,804.1

$

2,857.7

$

3,084.8

Refinery costs of sales

2,252.1

2,455.9

287.2

3,204.1

2,370.7

2,379.3

Refinery gross product margin

$

278.6

$

343.9

$

25.0

$

600.0

$

487.0

$

705.5

Throughput (barrels)

29.8

26.8

2.5

29.6

22.0

22.4

Refinery gross product margin per barrel of throughput

$

9.36

$

12.86

$

9.94

$

20.26

$

22.11

$

31.52

(4)

We use the Group 3 3:2:1 crack spread as a benchmark for our refinery. The Group 3 3:2:1 crack spread is expressed in dollars per barrel and is a proxy for the per
barrel margin that a sweet crude oil refinery would earn assuming it produced and sold at PADD II Group 3 prices the benchmark production of two barrels of gasoline and one barrel of ultra low sulfur diesel for every three barrels of light, sweet
crude oil input. For more information about the Group 3 3:2:1 crack spread see Managements Discussion and Analysis of Financial Condition and Results of OperationsMajor Influences on Results of Operations.

Our SPP Refinery 3:2:1 crack spread is derived using a similar methodology as the Group 3 3:2:1 crack spread and
is calculated by taking the sum of (i) two times our weighted average per barrel price received for our gasoline products plus (ii) our average per barrel price received for distillate, divided by three; then subtracting from that sum our
weighted average cost of crude oil supply per barrel. The SPP Refinery 3:2:1 crack spread is not a full representation of our realized refinery gross product margin because the Group 3 3:2:1 crack spread is composed only of gasoline and distillate,
whereas our refinery gross product margin is calculated using all of our refined products including asphalt and other lower margin products.

(5)

Retail fuel margin per gallon is calculated by dividing retail fuel gross margin by the fuel gallons sold at company-operated stores. Retail fuel gross margin is a
non-GAAP performance measure that we believe is important to investors in evaluating our retail performance. Our calculation of retail fuel gross margin may differ from similar calculations of other companies in our industry, thereby limiting its
usefulness as a comparative measure.

The following table shows the reconciliation of retail gross margin to retail segment
operating income for the year ended December 31, 2009, for the eleven months ended November 30, 2010, the 2010 Successor Period and the year ended December 31, 2011 and the nine months ended September 30, 2011 and 2012:

Investing in our common units involves a high degree of risk. You should carefully consider the risks described below together with
the other information set forth in this prospectus before making an investment decision. Any of the following risks and uncertainties could have a material adverse effect on our business, financial condition, cash flows and results of operations
could be materially adversely affected. If that occurs, we might not be able to pay distributions on our common units, the trading price of our common units could decline materially, and you could lose all or part of your investment. Although many
of our business risks are comparable to those faced by a corporation engaged in a similar business, limited partner interests are inherently different from the capital stock of a corporation and involve additional risks described below. The risks
discussed below are not the only risks we face. We may experience additional risks and uncertainties not currently known to us, or as a result of developments occurring in the future. Conditions that we currently deem to be immaterial may also
materially and adversely affect our business, financial condition, cash flows and results of operations, and our ability to pay distributions to unitholders.

Risks Related to Our Business and Industry

General Business and Industry Risks

We may not have sufficient available cash to pay any quarterly distribution on our units.

We may not have sufficient available cash each quarter to enable us to pay any distributions to our unitholders. The amount we will be
able to distribute on our common units principally depends on the amount of cash we generate from our operations, which is primarily dependent upon the operating margins we generate. Our operating margins, and thus, the cash we generate from
operations have been volatile, and we expect that they will fluctuate from quarter to quarter based on, among other things:



the cost of refining feedstocks, such as crude oil, that are processed and blended into refined products;



the price at which we are able to sell refined products;



the level of our direct operating expenses, including expenses such as employee and contract labor, maintenance and energy costs;



non-payment or other non-performance by our customers and suppliers; and



overall economic and local market conditions.

In addition, the actual amount of cash we will have available for distribution will depend on other factors, some of which are beyond our control, including:



the level of capital expenditures we make;



our debt service requirements;



the amount of any accrued but unpaid expenses;



the amount of any reimbursement of expenses incurred by our general partner and its affiliates;



fluctuations in our working capital needs;



our ability to borrow funds and access capital markets;



planned and unplanned maintenance at our facility, which, based on determinations by the board of directors of our general partner to maintain
reserves, may negatively impact our cash flows in the quarter in which such maintenance occurs;



restrictions on distributions and on our ability to make working capital borrowings; and

Our partnership agreement will not require us to pay a minimum quarterly distribution. The
amount of distributions that we pay, if any, and the decision to pay any distribution at all, will be determined by the board of directors of our general partner. Our quarterly distributions, if any, will be subject to significant fluctuations based
on the above factors.

For a description of additional restrictions and factors that may affect our ability to pay
distributions, see Managements Discussion and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesOur Distribution Policy.

Restrictions in the agreements governing our indebtedness could limit our ability to make distributions to our unitholders.

Subject to certain exceptions, the indenture governing the 2020 Notes and our revolving credit facility prohibit us from making
distributions to unitholders if certain defaults exist. In addition, both the indenture and our revolving credit facility contain additional restrictions limiting our ability to pay distributions to unitholders. Subject to certain exceptions, the
restricted payments covenant under the indenture restricts us from making cash distributions unless our fixed charge coverage ratio, as defined in the indenture, is at least 1.75 to 1.0 after giving pro forma effect to such distributions. Our
revolving credit facility generally restricts our ability to make cash distributions if we fail to have excess availability under the facility at least equal to the greater of (1) 25% of the lesser of (x) the $300 million commitment amount
and (y) the then applicable borrowing base and (2) $37.5 million. Accordingly, we may be restricted by our debt agreements from distributing all of our available cash to our unitholders. See Managements Discussion and
Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesDescription of Our Indebtedness.

The amount of our quarterly distributions, if any, will vary significantly both quarterly and annually and will be directly dependent on the
performance of our business. Unlike most publicly traded partnerships, we will not have a minimum quarterly distribution or employ structures intended to consistently maintain or increase distributions over time.

Investors who are looking for an investment that will pay predictable quarterly distributions should not invest in our common units. We
expect our business performance will be more cyclical and volatile, and our cash flows will be less stable, than the business performance and cash flows of most publicly traded partnerships. As a result, our quarterly distributions will be cyclical
and volatile and are expected to vary quarterly and annually. Unlike most publicly traded partnerships, we will not have a minimum quarterly distribution or employ structures intended to consistently maintain or increase distributions over time. The
amount of our quarterly distributions will be dependent on the performance of our business, which will be volatile as a result of fluctuations in the price of crude oil and other feedstocks and the demand for our finished products. Because our
quarterly distributions will be subject to significant fluctuations directly related to the available cash we generate, future quarterly distributions paid to our unitholders will vary significantly from quarter to quarter and may be zero. See
Managements Discussion and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesOur Distribution Policy.

The amount of cash we have available for distribution to unitholders depends primarily on our cash flow and not solely on profitability.

The amount of cash we have available for distribution depends primarily upon our cash flow and not solely on profitability, which may be
affected by non-cash items. For example, we may have working capital changes as well as extraordinary capital expenditures and major maintenance expenses in the future. See Managements Discussion and Analysis of Financial Condition and
Results of OperationLiquidity and Capital ResourcesCapital Spending. While these items may not affect our profitability in a quarter, they would reduce the amount of cash available for distribution with respect to such quarter. As
a result, we may make cash distributions during periods when we report losses and may not make cash distributions during periods when we report net income.

The board of directors of our general partner may modify or revoke our distribution policy at any time
at its discretion. Our partnership agreement does not require us to pay any distributions at all.

The board of
directors of our general partner adopted a distribution policy pursuant to which we will distribute an amount equal to the available cash we generate each quarter. However, the board may change such policy at any time at its discretion and could
elect not to pay distributions for one or more quarters. See Managements Discussion and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesOur Distribution Policy.

Our partnership agreement does not require us to pay any distributions at all. Accordingly, investors are cautioned not to place undue
reliance on the permanence of such a policy in making an investment decision. Any modification or revocation of our distribution policy could substantially reduce or eliminate the amounts of distributions to our unitholders. The amount of
distributions we make, if any, and the decision to make any distribution at all will be determined by the board of directors of our general partner, whose interests may differ from those of our public unitholders. Our general partner has limited
fiduciary and contractual duties, which may permit it to favor its own interests or the interests of its owners, including ACON Refining and TPG Refining, to the detriment of our public unitholders.

We may have capital needs for which our internally generated cash flows and other sources of liquidity may not be adequate.

If we cannot generate sufficient cash flows or otherwise secure sufficient liquidity to support our short-term and long-term capital
requirements, we may not be able to meet our payment obligations, comply with certain deadlines related to environmental regulations and standards or pursue our business strategies, any of which could have a material adverse effect on our results of
operations or liquidity. We have substantial short-term capital needs and may have substantial long-term capital needs. Our short-term working capital needs are primarily related to financing our refined product inventory and accounts receivable.
Our long-term needs for cash include those to support ongoing capital expenditures for equipment maintenance and upgrades during turnarounds at our refinery and to complete our routine and normally scheduled maintenance, regulatory and security
expenditures. We currently expect our next major turnaround to occur in 2013, for which we have budgeted approximately $50 million. The refinery is currently expected to have reduced throughputs during the months of April and October 2013 to
complete the turnaround. In addition, from time to time, we are required to spend significant amounts for repairs when one or more processing units experiences temporary shutdowns. We continue to utilize significant capital to upgrade equipment,
improve facilities, and reduce operational, safety and environmental risks. We may incur substantial compliance costs in connection with any new environmental, health and safety regulations. In addition, the board of directors of our general partner
has adopted a distribution policy pursuant to which we will distribute an amount equal to the available cash we generate each quarter to unitholders. As a result, we will need to rely on external financing sources, including commercial bank
borrowings and the issuance of debt and equity securities, to fund our growth. Our liquidity will affect our ability to satisfy any of these needs.

Our liquidity may be adversely affected by a reduction in third party credit.

We rely on third party credit for approximately 50% of our crude oil and other feedstock purchases. We purchase the remaining crude oil and other feedstocks daily on terms via a crude oil supply and
logistics agreement with JPM CCC, which provides logistical and administrative support to us for both the crude oil we source from them as well as the crude oil we source from our suppliers. For crude oil purchased on third party credit terms, we
pay for both domestic crude oil purchases and Canadian crude oil purchases during the month following delivery. If our suppliers who sell crude oil and other feedstocks to us on trade credit were to reduce or eliminate our credit lines, we would be
required to fund our purchases through our revolving credit facility or our crude oil supply and logistics agreement with JPM CCC, which would have a negative impact on liquidity.

Our arrangements with Marathon expose us to Marathon-related credit and performance risk.

We have a contract with Marathon under which we supply substantially all of the gasoline and diesel requirements for
the 90 independently owned and operated Marathon branded stores in our marketing area. Marathon has indemnification obligations to us pursuant to the agreements entered into in connection with the Marathon Acquisition. Marathons
indemnification obligation resulting from any breach of representations and warranties generally are limited by an indemnification deductible of $25 million and an indemnification ceiling of $100 million and are guaranteed by Marathon Petroleum.

Marathon Petroleum has guaranteed the performance of all of Marathons obligations under all of the acquisition
agreements entered into in connection with the Marathon Acquisition obligations discussed above. Nevertheless, relying on Marathons ability to honor its fuel requirements purchase obligations and indemnity obligations, and on Marathon
Petroleums ability to honor its guaranty obligations, exposes us to Marathons and Marathon Petroleums respective credit and business risks. There can be no assurance that claims resulting from any breach of Marathons
representations and warranties under the acquisition agreements entered into in connection with the Marathon Acquisition will not exceed the $100 million indemnification ceiling. Moreover, selling products to Marathon under the supply contract can
expose us to Marathons credit and general business risks. An adverse change in Marathons or Marathon Petroleums business, results of operations or financial condition could adversely affect their respective ability to perform each
of these obligations, which could consequently have a material adverse effect on our business, results of operations or liquidity and, as a result, our ability to make distributions.

Our historical financial statements may not be indicative of future performance.

The historical financial statements for periods prior to December 1, 2010 presented in this prospectus reflect carve-out financial statements of several operating units of Marathon, which, except for
certain assets that were not acquired (e.g., cash other than in-store cash at our convenience stores and receivables and assets sold to third parties) and certain liabilities (e.g., accounts payable, payroll and benefits payable and deferred taxes)
that were not assumed in connection with the Marathon Acquisition, represent the assets and liabilities that were transferred to us upon the closing of the Marathon Acquisition. We now own the assets and operate them as a standalone business. Prior
to the closing of the Marathon Acquisition, we had no history of operating these assets, and they were never operated as a standalone business, thus the historical results presented in the financial statements for the periods prior to the Marathon
Acquisition are not necessarily comparable to our financial statements following the Marathon Acquisition or indicative of the results for any future period. Additionally, we entered into certain arrangements at the closing of the Marathon
Acquisition, including our crude oil supply and logistics agreement with JPM CCC and a lease arrangement with Realty Income Properties 3 LLC (Realty Income), that resulted in our working capital needs and operating costs varying from
those affecting the assets that we acquired from Marathon. The pre-Marathon Acquisition historical financial information reflects intercompany allocations of expenses which may not be indicative of the actual expenses that would have been incurred
had the combined businesses been operating as a company independent from Marathon for the periods presented. In addition, our results of operations for periods subsequent to the closing of our initial public offering may not be comparable to our
results of operations for periods prior to the closing of our initial public offering as a result of certain transactions undertaken in connection with our initial public offering. See Managements Discussion and Analysis of Financial
Condition and Results of OperationsComparability of Historical Results for a discussion of factors that affect comparability. As a result, it is difficult to evaluate our historical results of operations to assess our future prospects
and viability.

Competition from companies having greater financial and other resources than we do could materially and adversely affect
our business and results of operations.

Our refining operations compete with domestic refiners and marketers in the
PADD II region of the United States, as well as with domestic refiners in other PADD regions and foreign refiners that import products into the United States. In addition, we compete with producers and marketers in other industries that supply
alternative forms of energy and fuels to satisfy the requirements of our industrial, commercial and individual customers. Certain of our competitors have larger, more complex refineries, and may be able to realize lower

per-barrel costs or higher margins per barrel of throughput. Several of our principal competitors are integrated national or international oil companies that are larger and have substantially
greater resources than we do and have access to proprietary sources of controlled crude oil production. Unlike these competitors, we obtain substantially all of our feedstocks from unaffiliated sources. Because of their integrated operations and
larger capitalization, these companies may be more flexible in responding to volatile industry or market conditions, such as shortages of crude oil supply and other feedstocks or intense price fluctuations.

Newer or upgraded refineries will often be more efficient than our refinery, which may put us at a competitive disadvantage. While we
have taken significant measures to maintain and upgrade units in our refinery by installing new equipment and repairing equipment to improve our operations, these actions involve significant uncertainties, since upgraded equipment may not perform at
expected throughput levels, the yield and product quality of new equipment may differ from design specifications and modifications may be needed to correct equipment that does not perform as expected. Any of these risks associated with new
equipment, redesigned older equipment or repaired equipment could lead to lower revenues or higher costs or otherwise have an adverse effect on future results of operations and financial condition and our ability to make distributions. Over time,
our refinery may become obsolete, or be unable to compete, because of the construction of new, more efficient facilities by our competitors.

Our retail operations compete with numerous convenience stores, gasoline service stations, supermarket chains, drug stores, fast food operations and other retail outlets. Increasingly, national
high-volume grocery and dry-goods retailers are entering the gasoline retailing business. Many of these competitors are substantially larger than we are. Because of their diversity, integration of operations and greater resources, these companies
may be better able to withstand volatile market conditions or levels of low or no profitability. In addition, these retailers may use promotional pricing or discounts, both at the pump and in the store, to encourage in-store merchandise sales. These
activities by our competitors could adversely affect our profit margins. Additionally, our convenience stores could lose market share, relating to both gasoline and merchandise, to these and other retailers, which could adversely affect our
business, results of operations and cash flows. Our convenience stores compete in large part based on their ability to offer convenience to customers. Consequently, changes in traffic patterns and the type, number and location of competing stores
could result in the loss of customers and reduced sales and profitability at affected stores, and adversely affect our ability to make distributions.

Difficult conditions in the U.S. and worldwide economies, and potential further deteriorating conditions in the United States and globally, may materially adversely affect our business, results of
operations and financial condition.

Continued volatility and disruption in worldwide capital and credit markets and
potential further deteriorating conditions in the United States and globally could affect our revenues and earnings negatively and could have a material adverse effect on our business, results of operations, financial condition and our ability to
make distributions. We are indirectly exposed to risks faced by our suppliers, customers and other business partners. The impact on these constituencies of the risks posed by continued economic turmoil have included, or can include, interruptions or
delays in the performance by counterparties to our contracts, reductions and delays in customer purchases, delays in or the inability of customers to obtain financing to purchase our products and the inability of customers to pay for our products.
All of these events may significantly adversely impact our business, results of operations and financial condition and, as a result, our ability to make distributions.

The geographic concentration of our refinery and retail assets creates a significant exposure to the risks of the local economy and other local adverse conditions. The location of our refinery also
creates the risk of significantly increased transportation costs should the supply/demand balance change in our region such that regional supply exceeds regional demand for refined products.

As our refinery and a significant number of our stores are located in Minnesota, Wisconsin and South Dakota, we primarily market our
refined and retail products in a single, relatively limited geographic area. As a

result, we are more susceptible to regional economic conditions than the operations of more geographically diversified competitors, and any unforeseen events or circumstances that affect our
operating area could also materially adversely affect our revenues and our ability to make distributions. These factors include, among other things, changes in the economy, weather conditions, demographics and population.

Should the supply/demand balance shift in our region as a result of changes in the local economy discussed above, an increase in refining
capacity or other reasons, resulting in supply in the PADD II region exceeding demand, we would have to deliver refined products to customers outside of the region and thus incur considerably higher transportation costs, resulting in lower refining
margins, if any. Changes in market conditions could have a material adverse effect on our business, financial condition and results of operations and, as a result, our ability to make distributions.

Our operating results are seasonal and generally significantly lower in the first and fourth quarters of the year for our refining business and in
the first quarter of the year for our retail business. We depend on favorable weather conditions in the spring and summer months.

Demand for gasoline is generally higher during the summer months than during the winter months due to seasonal increases in highway traffic. Decreased demand during the winter months can lead to lower
gasoline prices. As a result, the operating results of our refining business for the first and fourth calendar quarters are generally significantly lower than those for the second and third calendar quarters of each year.

Seasonal fluctuations in traffic also affect sales of motor fuels and merchandise in our retail fuel and convenience stores. As a result,
the operating results of our retail business are generally lower for the first quarter of the year. Weather conditions in our operating area also have a significant effect on our retail operating results. Customers are more likely to purchase higher
profit margin items at our retail fuel and convenience stores, such as fast foods, fountain drinks and other beverages and more gasoline during the spring and summer months, thereby typically generating higher revenues and gross margins for us in
these periods. Unfavorable weather conditions during these months and a resulting lack of the expected seasonal upswings in traffic and sales could have a material adverse effect on our business, financial condition and results of operations.

As the amount of cash we will be able to distribute with respect to a quarter principally depends on the amount of cash we
generate from operations and because we do not intend to reserve or borrow cash to pay distributions in subsequent quarters, distributions with respect to the first and fourth quarters of the year may be significantly lower than with respect to the
second and third quarters.

Weather conditions and natural disasters could materially and adversely affect our business and operating
results.

The effects of weather conditions and natural disasters can lead to volatility in the costs and availability
of energy and raw materials or negatively impact our operations or those of our customers and suppliers, which could have a significant adverse effect on our business and results of operations and, as a result, our ability to make distributions.

We may not be able to successfully execute our strategy of growth within the refining and retail industry through acquisitions.

A component of our growth strategy is to selectively consider accretive acquisitions within the refining industry and
retail market based on sustainable performance of the targeted assets through the refining cycle, access to advantageous crude oil supplies, attractive demand and supply market fundamentals, access to distribution and logistics infrastructure and
potential operating synergies. Our ability to do so will be dependent upon a number of factors, including our ability to identify acceptable acquisition candidates, consummate acquisitions on favorable terms, successfully integrate acquired assets
and obtain financing to fund acquisitions

We may not be successful in acquiring additional assets, and any acquisitions that we do consummate may not produce the anticipated
benefits or may have adverse effects on our business and operating results.

Our business may suffer if any of the executive officers of
our general partner or other key employees discontinues employment with us. Furthermore, a shortage of skilled labor or disruptions in our labor force may make it difficult for us to maintain labor productivity.

Our future success depends to a large extent on the services of the executive officers of our general partner and other key employees and
on our continuing ability to recruit, train and retain highly qualified employees in all areas of our operations, including accounting, business operations, finance and other key back-office and mid-office personnel. Furthermore, our operations
require skilled and experienced employees with proficiency in multiple tasks. The competition for these employees is intense, and the loss of these executives or employees could harm our business. If any of these executives or other key personnel
resign or become unable to continue in their present roles and are not adequately replaced, our business could be materially adversely affected. We do not maintain, nor do we plan to obtain, any insurance against the loss of any of these
individuals.

Our business is highly dependent on financial, accounting and other data processing systems and other communications
and information systems, including our enterprise resource planning tools. We process a large number of transactions on a daily basis and rely upon the proper functioning of computer systems. If a key system were to fail or experience unscheduled
downtime for any reason, even if only for a short period, our operations and financial results could be affected adversely. Our systems could also be damaged or interrupted by a security breach, fire, flood, power loss, telecommunications failure or
similar event. Our formal disaster recovery plan may not prevent delays or other complications that could arise from an information systems failure. Further, our business interruption insurance may not compensate us adequately for losses that may
occur.

We may incur significant liability under, or costs and capital expenditures to comply with, environmental, health and safety
regulations, which are complex and change frequently.

Our refinery, pipelines and retail operations are subject to
federal, state and local laws regulating, among other things, the generation, storage, handling, use and transportation of petroleum and hazardous substances, the

emission and discharge of materials into the environment, waste management, characteristics and composition of gasoline and diesel and other matters otherwise relating to the protection of the
environment. Our operations are also subject to various laws and regulations relating to occupational health and safety. Compliance with the complex array of federal, state and local laws relating to the protection of the environment, health and
safety is difficult and likely will require us to make significant expenditures. Moreover, our business is inherently subject to accidental spills, discharges or other releases of petroleum or hazardous substances into the environment including at
neighboring areas or third party storage, treatment or disposal facilities. For example, we have performed remediation of known soil and groundwater contamination beneath certain of our retail locations primarily as a result of leaking underground
storage tanks, and we will continue to perform remediation of this known contamination until the appropriate regulatory standards have been achieved. Certain environmental laws impose joint and several liability without regard to fault or the
legality of the original conduct in connection with the investigation and cleanup of such spills, discharges or releases. As such, we may be required to pay more than our fair share of such investigation or cleanup. We may not be able to operate in
compliance with all applicable environmental, health and safety laws, regulations and permits at all times. Violations of applicable legal or regulatory requirements could result in substantial fines, criminal sanctions, permit revocations,
injunctions and/or facility shutdowns. We may also be required to make significant capital expenditures or incur increased operating costs or change operations to achieve compliance with applicable standards.

We cannot predict the extent to which additional environmental, health and safety legislation or regulations will be enacted or become
effective in the future or how existing or future laws or regulations will be administered or interpreted with respect to our operations. Many of these laws and regulations are becoming increasingly stringent, and the cost of compliance with these
requirements can be expected to increase over time. For example, on September 12, 2012, the U.S. Environmental Protection Agency (EPA) published final amendments to the New Source Performance Standards (NSPS) for
petroleum refineries to be effective November 13, 2012. These amendments include standards for emissions of nitrogen oxides from process heaters and work practice standards and monitoring requirements for flares. To comply with the amendments,
we plan to install and operate a continuous emissions monitoring system for nitrogen oxides on a process heater. We have already installed and will operate additional instrumentation on our flare. We anticipate the total cost for these two projects
will be approximately $700,000 to be spent in 2012 and 2013. We continue to evaluate the regulation and amended standards, as may be applicable to the operations at our refinery. We cannot currently predict what additional costs that we may have to
incur, if any, to comply with the amended NSPS, but the costs could be material. In addition, the EPA has announced that it plans to propose new Tier 3 motor vehicle emission and fuel standards sometime in the second half of 2012. It has
been reported that these new Tier 3 regulations may, among other things, lower the maximum average sulfur content of gasoline from 30 parts per million to 10 parts per million. If the Tier 3 regulations are eventually implemented and lower the
maximum allowable content of sulfur or other constituents in fuels that we produce, we may at some point in the future be required to make significant capital expenditures and/or incur materially increased operating costs to comply with the new
standards. Expenditures or costs for environmental, health and safety compliance could have a material adverse effect on our results of operations, financial condition and profitability and, as a result, our ability to make distributions.

We could incur significant costs in cleaning up contamination at our refinery, terminal and convenience stores.

Our refinery site has been used for refining activities for many years. Petroleum hydrocarbons and various substances have been released
on or under our refinery site. Marathon performed remediation of known soil and groundwater contamination beneath the refinery for many years, and we will continue to perform remediation of this known contamination until the appropriate regulatory
standards have been achieved. These remediation efforts are being overseen by the Minnesota Pollution Control Agency (MPCA) pursuant to a remediation settlement agreement entered into by the former owner and MPCA in 2007. Releases of
petroleum hydrocarbons have also occurred at several of our convenience stores, and we have performed and will continue to perform remediation of this known contamination until the applicable regulatory standards are met. Costs for such

remediation activities are often unpredictable, and there can be no assurance that the future costs will not be material. It is possible that we may identify additional contamination in the
future, which could result in additional remediation obligations and expenses, including fines and penalties.

We are subject to strict
laws and regulations regarding employee and business process safety, and failure to comply with these laws and regulations could have a material adverse effect on our results of operations and financial condition.

We are subject to the requirements of OSHA and comparable state statutes that regulate the protection of the health and safety of workers.
In addition, OSHA requires that we maintain information about hazardous materials used or produced in our operations and that we provide this information to employees, state and local governmental authorities, and local residents. Failure to comply
with OSHA requirements, including general industry standards, process safety standards and control of occupational exposure to regulated substances, could subject us to significant fines or cause us to spend significant amounts on compliance, which
could have a material adverse effect on our results of operations, financial condition and the cash flows of the business and, as a result, our ability to make distributions.

Compliance with and changes in tax laws could adversely affect our performance.

We are subject to extensive tax liabilities, including federal, state and transactional taxes such as excise, sales/use, payroll, franchise, withholding and ad valorem taxes. New tax laws and regulations
and changes in existing tax laws and regulations are continuously being enacted or proposed that could result in increased expenditures for tax liabilities in the future. Certain of these liabilities are subject to periodic audits by the respective
taxing authority, which could increase our tax liabilities. Subsequent changes to our tax liabilities as a result of these audits may also subject us to interest and penalties. Any such changes in our tax liabilities could adversely affect our
ability to make distributions to our unitholders.

Our insurance policies may be inadequate or expensive.

Our insurance coverage does not cover all potential losses, costs or liabilities. We could suffer losses for uninsurable or uninsured
risks or in amounts in excess of our existing insurance coverage. Our ability to obtain and maintain adequate insurance may be affected by conditions in the insurance market over which we have no control. In addition, if we experience insurable
events, our annual premiums could increase further or insurance may not be available at all or if it is available, on restrictive coverage items. The occurrence of an event that is not fully covered by insurance or the loss of insurance coverage
could have a material adverse effect on our business, financial condition, and results of operations and, as a result, our ability to make distributions.

In the future, we may incur significant indebtedness in order to make future acquisitions or to develop our properties. Our level of indebtedness could affect our operations in several ways, including the
following:



a significant portion of our cash flows could be used to service our indebtedness;



a high level of debt would increase our vulnerability to general adverse economic and industry conditions;

a high level of debt may place us at a competitive disadvantage compared to our competitors that are less leveraged, and therefore may be able to take
advantage of opportunities that our indebtedness would prevent us from pursuing;



our debt covenants may also affect our flexibility in planning for, and reacting to, changes in the economy and in our industry;

a high level of debt may make it more likely that a reduction in our borrowing base following a periodic redetermination could require us to repay a
portion of our then-outstanding bank borrowings; and



a high level of debt may impair our ability to obtain additional financing in the future for working capital, capital expenditures, acquisitions,
general corporate or other purposes.

As of September 30, 2012, after giving effect to the 2020 Notes
offering and the use of proceeds therefrom, as described in Recent Developments2020 Notes Offering and Tender Offer:



we would have had $275 million of secured indebtedness, representing the 2020 Notes, and $118 million of obligations under our hedging
arrangements (of which $77 million represents the fair market value of contracts outstanding at September 30, 2012); and



we would have had commitments under the ABL Facility of $300 million (less approximately $24 million in outstanding letters of credit).

A high level of indebtedness increases the risk that we may default on our debt obligations. Our ability to
meet our debt obligations and to reduce our level of indebtedness depends on our future performance. General economic conditions and financial, business and other factors affect our operations and our future performance. Many of these factors are
beyond our control. We may not be able to generate sufficient cash flows to pay the interest on our debt, and future working capital, borrowings or equity financing may not be available to pay or refinance such debt. Factors that will affect our
ability to raise cash through an offering of our units or a refinancing of our debt include financial market conditions, the value of our assets and our performance at the time we need capital.

In addition, our bank borrowing base is subject to periodic redeterminations. We could be forced to repay a portion of our bank
borrowings due to redeterminations of our borrowing base. If we are forced to do so, we may not have sufficient funds to make such repayments. If we do not have sufficient funds and are otherwise unable to negotiate renewals of our borrowings or
arrange new financing, we may have to sell significant assets. Any such sale could have a material adverse effect on our business and financial condition and, as a result, our ability to make distributions.

Increased costs of capital could adversely affect our business.

Our business and operating results can be harmed by factors such as the availability, terms and cost of capital, increases in interest rates or a reduction in credit rating. Changes in any one or more of
these factors could cause our cost of doing business to increase, limit our access to capital, limit our ability to pursue acquisition opportunities, reduce our cash flows and place us at a competitive disadvantage. Recent and continuing disruptions
and volatility in the global financial markets may lead to an increase in interest rates or a contraction in credit availability impacting our ability to finance our operations.

Additionally, as with other yield-oriented securities, we expect that our unit price will be impacted by the level of our quarterly cash
distributions and implied distribution yield. The distribution yield is often used by investors to compare and rank related yield-oriented securities for investment decision-making purposes. Therefore, changes in interest rates may affect the yield
requirements of investors who invest in our common units, and a rising interest rate environment could have a material adverse impact on our unit price and our ability to issue additional equity to fund our operations or to make acquisitions or to
incur debt as well as increasing our interest costs.

We require continued access to capital. In particular, the board of
directors of our general partner has adopted a distribution policy pursuant to which we will distribute an amount equal to the available cash we generate each quarter to unitholders. As a result, we will need to rely on external financing sources to
fund our growth. A significant reduction in the availability of credit could materially and adversely affect our ability to achieve our planned growth and operating results.

We do not have the same flexibility as other types of organizations to accumulate cash and equity to
protect against illiquidity in the future.

Unlike a corporation, our policy is to distribute all available cash
generated each quarter. Accordingly, if we experience a liquidity problem in the future, we may have difficulty satisfying our debt obligations.

Risks Primarily Related to Our Refining Business

The price volatility of crude oil,
other feedstocks, refined products and fuel and utility services may have a material adverse effect on our earnings, cash flows and liquidity and our ability to make distributions to our unitholders.

Our refining and retail earnings, cash flows and liquidity from operations depend primarily on the margin above operating expenses
(including the cost of refinery feedstocks, such as crude oil and natural gas liquids that are processed and blended into refined products) at which we are able to sell refined products. Refining is primarily a margin-based business and, to increase
earnings, it is important to maximize the yields of high value finished products while minimizing the costs of feedstock and operating expenses. When the margin between refined product prices and crude oil and other feedstock costs contracts, our
earnings, and cash flows are negatively affected. Refining margins historically have been volatile, and are likely to continue to be volatile, as a result of a variety of factors, including fluctuations in the prices of crude oil, other feedstocks,
refined products and fuel and utility services. For example, from January 2005 to September 2012, the price for NYMEX WTI crude oil fluctuated between $33.87 and $145.29 per barrel, while the price for U.S. Gulf Coast conventional gasoline
fluctuated between $39.16 per barrel and $140.08 per barrel. While an increase or decrease in the price of crude oil may result in a similar increase or decrease in prices for refined products, there may be a time lag in the realization of the
similar increase or decrease in prices for refined products. The effect of changes in crude oil prices on our refining margins therefore depends in part on how quickly and how fully refined product prices adjust to reflect these changes.

In addition, the nature of our business requires us to maintain substantial refined product inventories. Because refined products are
commodities, we have no control over the changing market value of these inventories. Our refined product inventory is valued at the lower of cost or market value under the last-in, first-out (LIFO), inventory valuation methodology. If
the market value of our refined product inventory were to decline to an amount less than our LIFO cost, we would record a write-down of inventory and a non-cash charge to cost of sales.

Prices of crude oil, other feedstocks and refined products depend on numerous factors beyond our control, including the supply of and
demand for crude oil, other feedstocks, gasoline, diesel, asphalt and other refined products. Such supply and demand are affected by, among other things:



changes in global and local economic conditions;



domestic and foreign demand for fuel products, especially in the United States, China and India;



worldwide political conditions, particularly in significant oil producing regions such as the Middle East, West Africa and Latin America;



the level of foreign and domestic production of crude oil and refined products and the volume of crude oil, feedstock and refined products imported
into the United States;



availability of and access to transportation infrastructure;



utilization rates of U.S. refineries;



the ability of the members of the Organization of Petroleum Exporting Countries to affect oil prices and maintain production controls;

local factors, including market conditions, weather conditions and the level of operations of other refineries and pipelines in our markets.

Our direct operating expense structure also impacts our earnings. Our major direct operating expenses
include employee and contract labor, maintenance and energy costs. Our predominant variable direct operating cost is energy, which is comprised primarily of fuel and other utility services. The volatility in costs of fuel, principally natural gas,
and other utility services, principally electricity, used by our refinery and other operations affect our operating costs. Fuel and utility prices have been, and will continue to be, affected by factors outside our control, such as supply and demand
for fuel and utility services in both local and regional markets. Natural gas prices have historically been volatile and, typically, electricity prices fluctuate with natural gas prices. Future increases in fuel and utility prices may have a
negative effect on our earnings and cash flows. Fuel and other utility services costs constituted approximately 13.0% and 13.3% of our total direct operating expenses for the nine months ended September 30, 2012 and the year ended
December 31, 2011, respectively.

Volatility in refined product prices also affects our borrowing base under our
revolving credit facility. A decline in prices of our refined products reduces the value of our refined product inventory collateral, which, in turn, may reduce the amount available for us to borrow under our revolving credit facility.

Our results of operations are affected by crude oil differentials, which may fluctuate substantially.

Our results of operations are affected by crude oil differentials, which may fluctuate substantially. Since 2010, refined product prices
have been more correlated to prices of Brent than to NYMEX WTI, the traditional U.S. crude oil benchmark, as the discount to which a barrel of NYMEX WTI traded relative to a barrel of Brent has widened significantly relative to historical levels.
This differential has also been very volatile as a result of various continuing geopolitical events as well as logistical and infrastructure constraints to move crude oil from Cushing, Oklahoma into the U.S. Gulf Coast. Between December 1, 2010
and September 30, 2012, the discount at which a barrel of NYMEX WTI traded relative to a barrel of Brent increased from $2.12 to $19.34. The widening of this price differential benefited refineries, such as ours, that are capable of sourcing
and utilizing crude oil that is priced more in line with NYMEX WTI. The refinery not only realized relatively lower feedstock costs but also was able to sell refined products at prices that had been pushed upward by higher Brent prices.

The dangers inherent in our operations could cause disruptions and could expose us to potentially significant losses, costs or liabilities and
reduce our liquidity. We are particularly vulnerable to disruptions in our operations because all of our refining operations are conducted at a single facility.

Our operations are subject to significant hazards and risks inherent in refining operations and in transporting and storing crude oil, intermediate products and refined products. These hazards and risks
include, but are not limited to, natural disasters, fires, explosions, pipeline ruptures and spills, third party interference and mechanical failure of equipment at our facilities, any of which could result in production and distribution
difficulties and disruptions, pollution (such as oil spills, etc.), personal injury or wrongful death claims and other damage to our properties and the property of others. For example, in December 2007, a fuel oil tank roof caught on fire at our
refinery when an operator was attempting to thaw a level gauge. The tanks roof was destroyed and the operator was fatally injured during the fire.

There is also risk of mechanical failure and equipment shutdowns both in the normal course of operations and following unforeseen events. In such situations, undamaged refinery processing units may be
dependent on, or interact with, damaged process units and, accordingly, are also subject to being shut down. For example, on

May 6, 2012, our refinery experienced a temporary shutdown due to a power outage that appears to have originated from outside the plant as a result of high winds and thunderstorms. In the
case of such a shutdown, the refinery must initiate a standard start-up process, and such process typically lasts several days. We were able to resume normal operations on May 13, 2012. Because all of our refining operations are conducted at a
single refinery, any of such events at our refinery could significantly disrupt our production and distribution of refined products, including the supply of our refined products to our convenience stores, which receive substantially all of their
supply of gasoline and diesel from the refinery. Any disruption in our ability to supply our convenience stores would increase the cost of purchasing refined products for our retail business. Any sustained disruption would have a material adverse
effect on our business, financial condition, results of operations and cash flows and, as a result, our ability to make distributions.

We are subject to interruptions of supply and distribution as a result of our reliance on pipelines for transportation of crude oil, blendstocks
and refined products.

Our refinery receives most of its crude oil and delivers a portion of its refined products
through pipelines. The Minnesota Pipeline system is the primary supply route for crude oil and has transported substantially all of the crude oil used at our refinery. We also distribute a portion of our transportation fuels through pipelines owned
and operated by Magellan Pipeline Company, L.P. (Magellan), including the Aranco Pipeline, which Magellan leases from us. We could experience an interruption of supply or delivery, or an increased cost of receiving crude oil and
delivering refined products to market, if the ability of these pipelines to transport crude oil, blendstocks or refined products is disrupted because of accidents, weather interruptions, governmental regulation, terrorism, other third party action
or any of the types of events described in the preceding risk factor. For example, there was a leak in 2006 prior to the completion of the expansion of the Minnesota Pipeline, and the refinery was temporarily shut off from any receipts from the
Minnesota Pipeline other than crude oil that was already in the tanks at Cottage Grove, Minnesota. At that time, the only alternative to receive crude oil was the Wood River Pipeline, a pipeline extending from Wood River, Illinois to a connection
with the Minnesota Pipeline near Pine Bend, Minnesota, which had limited capacity to meet the refinerys needs. While the refinery can receive crude oil deliveries from the Wood River Pipeline if the Minnesota Pipeline system experiences
another disruption, this would result in an increase in the cost of crude oil and therefore lower refining margins.

In
addition, due to the common carrier regulatory obligation applicable to interstate oil pipelines, capacity must be prorated among shippers in an equitable manner in accordance with the tariff then in effect in the event there are nominations in
excess of capacity. Therefore, nominations by new shippers or increased nominations by existing shippers may reduce the capacity available to us. Any prolonged interruption in the operation or curtailment of available capacity of the pipelines that
we rely upon for transportation of crude oil and refined products could have a material adverse effect on our business, financial condition, results of operations and cash flows and, as a result, our ability to make distributions.

We must make substantial capital expenditures on our operating facilities to maintain their reliability and efficiency. If we are unable to
complete capital projects at their expected costs and/or in a timely manner, or if the market conditions assumed in our project economics deteriorate, our financial condition, results of operations or cash flows, and our ability to make
distributions to unitholders, could be materially and adversely affected.

Delays or cost increases related to the
engineering, procurement and construction of new facilities (or improvements and repairs to our existing facilities and equipment) could have a material adverse effect on our business, financial condition or results of operations, and our ability to
make distributions to our unitholders. Such delays or cost increases may arise as a result of unpredictable factors in the marketplace, many of which are beyond our control, including:

Our refinery consists of many processing units, a number of which have been in operation for many years. Equipment, even if properly
maintained, may require significant capital expenditures and expenses to keep it operating at optimum efficiency. For example, as part of installing safety instrumentation systems throughout the refinery to improve operational and safety
performance, approximately $21 million was spent from 2006 through September 2012, and we have budgeted for additional related expenditures through 2013 to complete the instrumentation project. One or more of the units may require unscheduled
downtime for unanticipated maintenance or repairs that may be more frequent than our scheduled turnarounds for such units. Scheduled and unscheduled maintenance could reduce our revenues during the period of time that the units are not operating.
Our next major turnaround is scheduled for 2013 for which we have budgeted approximately $50 million. While we are still finalizing our planning for this turnaround, we currently expect the refinery to have reduced throughputs during the months of
April and October 2013 to complete the turnaround. We do not intend to reserve cash to pay distributions during periods of scheduled or unscheduled maintenance, though we do intend to reserve for turnaround expenses.

Any one or more of these occurrences could have a significant impact on our business. If we were unable to make up the delays or to
recover the related costs, or if market conditions change, it could materially and adversely affect our financial position, results of operations or cash flows and, as a result, our ability to make distributions.

A portion of our workforce is unionized, and we may face labor disruptions that would interfere with our operations.

Approximately 180 of our employees associated with the operations of our refining business are covered by a collective bargaining
agreement that expires in December 2013. In addition, 23 of our employees associated with the operations of our retail business are covered by a collective bargaining agreement that expires in August 2014. We may not be able to renegotiate our
collective bargaining agreements on satisfactory terms or at all when such agreements expire. A failure to do so may increase our costs associated with our workforce. Other employees of ours who are not presently represented by a union may become so
represented in the future as well. In 2006, the unionized refinery employees conducted a strike when Marathon sought to revise certain working terms and conditions. Another work stoppage resulting from, among other things, a dispute over a term or
condition of a collective bargaining agreement that covers employees who work at our refinery or in our retail business, could cause disruptions in our business and negatively impact our results of operations and ability to make distributions.

Product liability claims and litigation could adversely affect our business and results of operations.

Product liability is a significant commercial risk. Substantial damage awards have been made in certain jurisdictions against
manufacturers and resellers based upon claims for injuries caused by the use of or exposure to various products. Failure of our products to meet required specifications could result in product liability claims from our shippers and customers arising
from contaminated or off-specification commingled pipelines and storage tanks and/or defective quality fuels. There can be no assurance that product liability claims against us would not have a material adverse effect on our business or results of
operations and on our ability to make distributions.

Laws and regulations restricting emissions of greenhouse gases could force us to incur increased
capital and operating costs and could have a material adverse effect on our results of operations and financial condition.

In December 2009, the EPA determined that emissions of carbon dioxide, methane and other greenhouse gases (GHGs) endanger public health and the environment because emissions of
such gases are, according to the EPA, contributing to warming of the earths atmosphere and other climatic changes. Based on these findings, the EPA has begun adopting and implementing regulations to restrict emissions of GHGs under existing
provisions of the federal Clean Air Act, as amended (CAA). The EPA adopted two sets of rules effective January 2, 2011 regulating GHG emissions under the CAA, one of which requires a reduction in emissions of GHGs from motor
vehicles and the other of which regulates emissions of GHGs from certain large stationary sources. While the EPAs rules relating to emissions of GHGs from large stationary sources of emissions are currently subject to a number of legal
challenges, the federal courts have thus far declined to issue any injunctions to prevent the EPA from implementing or requiring state environmental agencies to implement the rules. The EPA has also implemented rules requiring the reporting of GHG
emissions from specified large GHG emission sources in the United States, including petroleum refineries, on an annual basis, for emissions occurring after January 1, 2010. Additionally, in December 2010, the EPA reached a settlement agreement
with numerous parties pursuant to which it agreed to promulgate NSPS for GHG emissions from petroleum refineries by November 2012. To date, the EPA has not proposed the NSPS for GHG emissions from petroleum refineries, and we cannot predict the
requirements of these rules. We may be required to make significant capital expenditures and/or incur materially increased operating costs to comply with the GHG NSPS once it is finalized by the EPA.

In addition, the U.S. Congress has from time to time considered adopting legislation to reduce emissions of GHGs, and almost one-half of
the states have already taken legal measures to reduce emissions of GHGs primarily through the planned development of GHG emission inventories and/or regional GHG cap and trade programs. These cap and trade programs generally work by requiring major
sources of emissions, such as electric power plants, or major producers of fuels, such as refineries and gas processing plants, to acquire and on an annual basis surrender emission allowances. The number of allowances available for purchase is
reduced over time in an effort to achieve the overall GHG emission reduction goal. Minnesota is a participant in the Midwest Regional GHG Reduction Accord, a non-binding resolution that could lead to the creation of a regional GHG cap-and-trade
program if the Minnesota legislature and the legislatures of other participating states enact implementing legislation.

The
adoption of legislation or regulatory programs to reduce emissions of GHGs could require us to incur increased operating costs, such as costs to purchase and operate emissions control systems, to acquire emissions allowances or comply with new
regulatory or reporting requirements. Any such legislation or regulatory programs could also increase the cost of consuming, and thereby reduce demand for, the refined products that we produce. Consequently, legislation and regulatory programs to
reduce emissions of GHGs could have an adverse effect on our business, financial condition and results of operations and, as a result, our ability to make distributions.

In addition, some scientists have concluded that increasing concentrations of GHGs in the Earths atmosphere may produce climate changes that have significant physical effects, such as increased
frequency and severity of storms, droughts, floods and other climatic events. If any such events were to occur, they could have an adverse effect on our business, financial condition and results of operations and, as a result, our ability to make
distributions.

Renewable fuels mandates may reduce demand for the petroleum fuels we produce, which could have a material adverse
effect on our results of operations and financial condition, and our ability to make distributions to our unitholders.

Pursuant to the Energy Policy Act of 2005 and the Energy Independence and Security Act of 2007, the EPA has issued Renewable Fuels
Standards (RFS) implementing mandates to blend renewable fuels into the

petroleum fuels produced and sold in the United States. Under RFS, the volume of renewable fuels that obligated refineries like us must blend into their finished petroleum fuels increases
annually over time until 2022. We currently purchase renewable identification number credits (RINS) for some fuel categories on the open market, as well as waiver credits for cellulosic biofuels from the EPA, in order to comply with the
RFS. In the future, we may be required to purchase additional RINS on the open market and waiver credits from the EPA to comply with the RFS. We cannot currently predict the future prices of RINS or waiver credits, but the costs to obtain the
necessary number of RINS and waiver credits could be material. Additionally, Minnesota law currently requires that all diesel sold in the state for use in internal combustion engines must contain at least 5% biodiesel. Under this statute, if certain
preconditions are met, the minimum biodiesel content in diesel sold in the state will increase to 10% beginning on May 1, 2012, and to 20% beginning on May 1, 2015. The increase to 10% did not occur on May 1, 2012, because the
Minnesota commissioners of agriculture, commerce, and pollution control did not certify that all statutory pre-conditions were satisfied by the statutory deadline, but instead jointly recommended delaying the increase to 10% by one year, to
May 1, 2013. Minnesota law also currently requires, with limited exceptions, that all gasoline sold or offered for sale in the state must contain the maximum amount of ethanol allowed under federal law for use in all gasoline-powered motor
vehicles. On October 13, 2010, the EPA granted a partial waiver raising the maximum amount of ethanol allowed under federal law from 10% to 15% for cars and light trucks manufactured since 2007, and on January 21, 2011, EPA extended the
maximum allowable ethanol content of 15% to apply to cars and light trucks manufactured since 2001. The maximum amount allowed under federal law currently remains at 10% ethanol for all other vehicles. EPA required that fuel and fuel additive
manufacturers take certain steps before introducing gasoline containing 15% ethanol (E15) into the market, including developing and obtaining EPA approval of a plan to minimize the potential for E15 to be used in vehicles and engines not
covered by the partial waiver. EPA has taken several recent actions to authorize the introduction of E15 into the market, including approving, on June 15, 2012, the first plans to minimize the potential for E15 to be used in vehicles and
engines not covered by the partial waiver. Existing laws and regulations could change, and the minimum volumes of renewable fuels that must be blended with refined petroleum fuels may increase. Because we do not produce renewable fuels, increasing
the volume of renewable fuels that must be blended into our products displaces an increasing volume of our refinerys product pool, potentially resulting in lower earnings and materially adversely affecting our ability to make distributions.

Our pipeline interests are subject to federal and/or state rate regulation, which could reduce our profitability.

Our pipeline transportation activities are subject to regulation by multiple governmental agencies, and compliance with such regulation
increases our cost of doing business and affects our profitability. Additional proposals and proceedings that affect the oil industry are regularly considered by Congress, the states, FERC and the courts. We cannot predict when or whether any such
proposals may become effective or what impact such proposals may have. Projected expenditures related to the Minnesota Pipeline reflect the recurring costs resulting from compliance with these regulations, and these costs may increase due to future
acquisitions, changes in regulation, changes in use, ongoing expenditures to maintain reliability and efficiency or discovery of existing but unknown compliance issues. In addition, if the current lease with Magellan of the Aranco Pipeline were
terminated and we were to operate the Aranco Pipeline or, if the Cottage Grove pipelines were required to comply with these regulations, we would incur similar costs.

The Minnesota Pipeline is a common carrier pipeline providing interstate transportation service, which is subject to regulation by FERC under the Interstate Commerce Act (ICA). The ICA
requires that tariff rates for interstate petroleum pipelines transportation service be just and reasonable and that the rates and terms of service of such pipelines not be unduly discriminatory or unduly preferential. The tariff rates are generally
set by the board of managers of the Minnesota Pipe Line Company, which we do not control. Because we currently do not operate the Minnesota Pipeline or control the board of managers of the Minnesota Pipe Line Company, we do not control how the
Minnesota Pipelines tariff is applied, including the tariff provisions governing the allocation of capacity, or control of decision-making with respect to tariff changes for the pipeline.

FERC can investigate the pipelines rates and certain terms of service on its own
initiative. In addition, shippers may file with FERC protests against new tariff rates and/or terms and conditions of service or complaints against existing tariff rates and/or terms and conditions of services. Under certain circumstances, FERC
could limit the Minnesota Pipe Line Companys ability to set rates based on its costs, or could order the Minnesota Pipe Line Company to reduce its rates and could require the payment of reparations to complaining shippers for up to two years
prior to the complaint or refunds to all shippers in the context of a protest proceeding. If it found the Minnesota Pipelines rates or terms of service to be contrary to statutory requirements, FERC could impose conditions it considers
appropriate and/or impose penalties. Further, FERC could declare pipeline-related facilities to be common carrier facilities and require that common carrier access be provided or otherwise alter the terms of service and/or rates of such facilities,
to the extent applicable. Rate regulation or a successful challenge to the rates the Minnesota Pipeline charges could adversely affect its financial position, cash flows, or results of operations and, thus, our financial position, cash flows or
results of operations. Conversely, reduced rates on the Minnesota Pipeline would reduce the rates for transportation of crude oil into our refinery.

FERC currently allows petroleum pipelines to change their rates within prescribed ceiling levels tied to an inflation index. The Minnesota Pipeline currently bases its rates on the indexing methodology.
If the Minnesota Pipeline were to attempt to increase rates beyond the maximum allowed by the indexing methodology, it would be required to file a cost-of-service justification, obtain approval from an unaffiliated party that intends to ship on the
pipeline (with respect to initial rates for any new service), obtain approval from all current shippers (i.e., settlement), or obtain prior approval to file market-based rates. FERCs indexing methodology is subject to review every five years.
In an order issued in December 2010, FERC announced that, effective July 1, 2011, the index would equal the change in the producer price index for finished goods plus 2.65% (previously, the index was equal to the change in the producer price
index for finished goods plus 1.3%). This index is to be in effect through July 2016. If the increases in the index are not sufficient to fully reflect actual increases to our costs, our financial condition could be adversely affected. If the index
results in a rate increase that is substantially in excess of the pipelines actual cost increases, or it results in a rate decrease that is substantially less than the pipelines actual cost decrease, the rates may be protested, and, if
such protests are successful, result in the lowering of the pipelines rates below the indexed level. FERCs rate-making methodologies may limit the pipelines ability to set rates based on our true costs and may delay or limit the
use of rates that reflect increased costs of providing transportation service.

If we were to operate the Aranco Pipeline to
provide transportation of crude oil or petroleum products in interstate commerce, we would expect to also be regulated by FERC as an interstate oil pipeline and the Aranco Pipeline would be subject to the same regulatory risks discussed above.

Terrorist attacks and other acts of violence or war may affect the market for our units, the industry in which we conduct our
operations and our results of operations and our ability to make distributions to our unitholders.

Terrorist attacks
may harm our business results of operations. We cannot provide assurance that there will not be further terrorist attacks against the United States or U.S. businesses. Such attacks or armed conflicts may directly impact our refinery, properties or
the securities markets in general. More generally, any of these events could cause consumer confidence and spending to decrease or result in increased volatility in the United States and worldwide financial markets and economy. Adverse economic
conditions could harm the demand for our products or the securities markets in general, which could harm our operating results and ability to make distributions.

While we have insurance that provides some coverage against terrorist attacks, such insurance has become increasingly expensive and difficult to obtain. As a result, insurance providers may not continue
to offer this coverage to us on terms that we consider affordable, or at all.

Some of our operations are conducted with partners, which may decrease our ability to manage risks
associated with those operations.

We sometimes enter into arrangements to conduct certain business operations, such as
pipeline transportation, with partners in order to share risks associated with those operations. However, these arrangements may also decrease our ability to manage risks and costs associated with those operations, particularly where we are not the
operator. We could have limited influence over and control of the behaviors and performance of these operations. This could affect our operational performance, financial position and reputation.

We own 17% of the outstanding common interests of the Minnesota Pipe Line Company and 17% of the outstanding preferred shares of MPL
Investments, Inc., which owns 100% of the preferred units of the Minnesota Pipe Line Company. The Minnesota Pipe Line Company owns the Minnesota Pipeline, a crude oil pipeline system in Minnesota that transports crude oil to the Twin Cities area and
which consistently transports most of our crude oil input. The remaining interests in the Minnesota Pipe Line Company are held by a subsidiary of Koch Industries, Inc., which operates the system and is an affiliate of the only other refinery owner
in Minnesota, with a 74.16% interest, and TROF Inc. with an 8.84% interest. For more information about the economic effect of our investments in the Minnesota Pipe Line Company and MPL Investments, see Managements Discussion and Analysis
of Financial Condition and Results of OperationsCritical Accounting Policies and Estimates and Results of Operations. Because our investments in the Minnesota Pipe Line Company and MPL Investments are limited, we do not
have significant influence over or control of the performance of the Minnesota Pipe Line Companys operations, which could impact our operational performance, financial position and reputation.

If we are unable to obtain our crude oil supply without the benefit of the crude oil supply and logistics agreement with JPM CCC or similar
agreement, our exposure to the risks associated with volatile crude oil prices may increase.

Our supply and logistics
agreement with JPM CCC allows us to price all crude oil processed at the refinery one day after it is received at the plant. This arrangement minimizes the amount of in-transit inventory and reduces our exposure to fluctuations in crude oil prices.
In excess of 90% of the crude oil delivered at the refinery is handled through our agreement with JPM CCC independent of whether crude oil is sourced from our suppliers or from JPM CCC directly. If we are unable to obtain our crude oil supply
through the crude oil supply and logistics agreement or similar agreement, our exposure to crude oil pricing risks may increase as the number of days between when we pay for the crude oil and when the crude oil is delivered to us increases. Such
increased exposure could negatively impact our liquidity position due to our increased working capital needs as a result of the increase in the value of crude oil inventory we would have to carry on our balance sheet and, therefore, could adversely
affect our ability to make distributions.

Our suppliers source a substantial amount of our crude oil from the Bakken Shale of North
Dakota and may experience interruptions of supply from that region.

Our suppliers source a substantial amount of our
crude oil from the Bakken Shale of North Dakota. As a result, we may be disproportionately exposed to the impact of delays or interruptions of supply from that region caused by transportation capacity constraints, curtailment of production,
unavailability of equipment, facilities, personnel or services, significant governmental regulation, natural disasters, adverse weather conditions, plant closures for scheduled maintenance or interruption of transportation of oil or natural gas
produced from the wells in that area.

We may enter into commodity derivatives contracts to mitigate our crack spread risk with respect
to a portion of our expected gasoline and diesel production. We enter into these arrangements with the intent to

secure a minimum fixed cash flow stream on the volume of products hedged during the hedge term. However, our hedging arrangements may fail to fully achieve these objectives for a variety of
reasons, including our failure to have adequate hedging contracts, if any, in effect at any particular time and the failure of our hedging arrangements to produce the anticipated results. We may not be able to procure adequate hedging arrangements
due to a variety of factors. Moreover, while intended to reduce the adverse effects of fluctuations in crude oil and refined product prices, such transactions may limit our ability to benefit from favorable changes in margins. In addition, our
hedging activities may expose us to the risk of financial loss in certain circumstances, including instances in which:



the volumes of our actual use of crude oil or production of the applicable refined products is less than the volumes subject to the hedging
arrangement;



accidents, interruptions in feedstock transportation, inclement weather or other events cause unscheduled shutdowns or otherwise adversely affect our
refinery, or those of our suppliers or customers;



the counterparties to our futures contracts fail to perform under the contracts; or



a sudden, unexpected event materially impacts the commodity or crack spread subject to the hedging arrangement.

As a result, the effectiveness of our risk mitigation strategy could have a material adverse impact on our financial results and our
ability to make distributions. See Managements Discussion and Analysis of Financial Condition and Results of OperationsQuantitative and Qualitative Disclosure About Market Risk.

In addition, these risk mitigation activities involve basis risk. Basis risk in a hedging arrangement occurs when the price of the
commodity we hedge is more or less variable than the index upon which the hedged commodity is based, thereby making the hedge less effective. For example, a NYMEX index used for hedging certain volumes of crude oil or refined products may have more
or less variability than the cost or price for such crude oil or refined products. We do not expect to hedge the basis risk inherent in our derivatives contracts.

Our commodity derivative activities could result in period-to-period earnings volatility.

We do not apply hedge accounting to our commodity derivative contracts and, as a result, unrealized gains and losses are charged to our earnings based on the increase or decrease in the market value of
the unsettled position. These gains and losses are reflected in our income statement in periods that differ from when the underlying hedged items (i.e., gross margins) are reflected in our income statement. Such derivative gains or losses in
earnings may produce significant period-to-period earnings volatility that is not necessarily reflective of our underlying operational performance.

Derivatives regulation included in current financial reform legislation could impede our ability to manage business and financial risks by restricting our use of derivative instruments as hedges
against fluctuating commodity prices.

The U.S. Congress adopted the Dodd-Frank Wall Street Reform and Consumer
Protection Act in 2010 (the Dodd-Frank Act). This comprehensive financial reform legislation establishes federal oversight and regulation of the over-the-counter derivatives market and entities, such as us, that participate in that
market. The legislation was signed into law by the President on July 21, 2010 and requires the Commodity Futures Trading Commission (CFTC) and the SEC to promulgate rules and regulations implementing the new legislation within 360
days from the date of enactment. In December 2011, the CFTC extended temporary exemptive relief from the deadline for certain regulations applicable to swaps until no later than July 16, 2012. The CFTC has since adopted regulations to set
position limits for certain futures and option contracts in the major energy markets. The CFTC has also proposed to establish minimum capital requirements, although it is not possible at this time to predict whether or when the CFTC will adopt these
rules as proposed or include comparable provisions in its rulemaking

under the Dodd-Frank Act. The Dodd-Frank Act may also require compliance with margin requirements and with certain clearing and trade-execution requirements in connection with certain derivative
activities, although the application of those provisions is uncertain at this time. The legislation may also require the counterparties to our commodity derivative contracts to spinoff some of their derivatives activities to a separate entity, which
may not be as creditworthy as the current counterparty, or cause the entity to comply with the capital requirements, which could result in increased costs to counterparties such as us.

The Dodd-Frank Act and any new regulations could significantly increase the cost of some commodity derivative contracts (including
through requirements to post collateral, which could adversely affect our available liquidity), materially alter the terms of some commodity derivative contracts, reduce the availability of some derivatives to protect against risks we encounter,
reduce our ability to monetize or restructure our existing commodity derivative contracts and potentially increase our exposure to less creditworthy counterparties. If we reduce our use of derivatives as a result of the Dodd-Frank Act and any new
regulations, our results of operations may become more volatile and our cash flows may be less predictable, which could adversely affect our ability to make distributions or plan for and fund capital expenditures. Increased volatility may make us
less attractive to certain types of investors. Finally, the Dodd-Frank Act was intended, in part, to reduce the volatility of oil and natural gas prices, which some legislators attributed to speculative trading in derivatives and commodity
instruments related to oil and natural gas. If the Dodd-Frank Act and any new regulations result in lower commodity prices, our revenues could be adversely affected. Any of these consequences could adversely affect our business, financial condition
and results of operations and therefore could have an adverse effect on our ability to make distributions.

Risks Primarily Related to Our
Retail Business

Our retail business depends on one principal supplier for a substantial portion of its merchandise inventory. A
change of merchandise suppliers, a disruption in merchandise supply, a significant change in our relationship with our principal merchandise supplier or material changes in the payment terms or availability of trade credit provided by our
merchandise suppliers could have a material adverse effect on our retail business and results of operations or liquidity.

Eby-Brown Company (Eby-Brown) is a wholesale grocer that has been the primary supplier of general merchandise, including most tobacco and grocery items, for all our retail stores since 1993.
For the nine months ended September 30, 2012 and the year ended December 31, 2011, our retail business purchased approximately 75% of its convenience store inside merchandise requirements from Eby-Brown. Our retail business also purchases
a variety of merchandise, including soda, beer, bread, dairy products, ice cream and snack foods, directly from a number of manufacturers and their wholesalers. A change of merchandise suppliers, a disruption in merchandise supply or a significant
change in our relationship with Eby-Brown could have a material adverse effect on our retail business and results of operations. In addition, our retail business is impacted by the availability of trade credit to fund merchandise purchases. Any
material changes in the payments terms, including payment discounts, or availability of trade credit provided by our merchandise suppliers could adversely affect our liquidity or results of operations and, as a result, our ability to make
distributions.

If the locations of our current convenience stores become unattractive to customers and attractive alternative locations
are not available for a reasonable price, then our ability to maintain and grow our retail business will be adversely affected.

We believe that the success of any retail store depends in substantial part on its location. There can be no assurance that the locations of our retail stores will continue to be attractive to customers
as demographic patterns change. Neighborhood or economic conditions where retail stores are located could decline in the future, resulting in potentially reduced sales in these locations. If we cannot obtain desirable locations at reasonable prices,
our ability to maintain and grow our retail business could be adversely affected, which could have an adverse effect on our business, financial condition or results of operations and, as a result, our ability to make distributions.

The growth of our retail business depends in part on our ability to open and profitably operate new
convenience stores and to successfully integrate acquired sites and businesses in the future.

We may not be able to
open new convenience stores and any new stores we open may be unprofitable. Additionally, acquiring sites and businesses in the future involves risks that could cause our actual growth or operating results to be lower than expected. If these events
were to occur, each would have a material adverse impact on our financial results. There are several factors that could affect our ability to open and profitably operate new stores or to successfully integrate acquired sites and businesses. These
factors include:



competition in targeted market areas;



difficulties during the acquisition process in discovering certain liabilities of the businesses that we acquire;



the inability to identify and acquire suitable sites or to negotiate acceptable leases for such sites;

limitations on investments contained in our revolving credit facility and other debt instruments;



difficulties in obtaining governmental and other third-party consents, permits and licenses needed to operate additional stores;



difficulties in obtaining any cost savings, accretion and financial improvements anticipated from future acquired stores or their integration; and



challenges associated with the consummation and integration of any future acquisition.

Our retail store franchisees are independent business operators that could take actions that harm our brand, reputation or goodwill, which could
adversely affect our business, results of operations, financial condition or cash flows.

Our retail store franchisees
are independent business operators, not employees, and, as such, we cannot control their operations. These franchisees could hire and fail to train unqualified sales associates and other employees, or operate the franchised retail stores in a manner
inconsistent with our operating standards. If our retail store franchisees provide diminished quality of service to customers, or if they engage or are accused of engaging in unlawful or tortious acts, such as sexual harassment or discriminatory
practices in violation of applicable laws, then our brand, reputation or goodwill could be harmed, which could have an adverse effect on our business, results of operations, financial condition or cash flows and, as a result, our ability to make
distributions.

Additionally, as independent business operators, our retail store franchisees could occasionally disagree with
us or with our strategies regarding our retail business or with our interpretation of the rights and obligations set forth under our retail franchise agreement. This could lead to disputes with our retail store franchisees, which we expect to occur
from time to time in the future as we continue to offer and sell retail store franchises. To the extent we have such disputes, the attention of our management and our retail store franchisees could be diverted, which could have an adverse effect on
our business, results of operations, financial condition or cash flows and, as a result, our ability to make distributions.

In connection with credit and debit card sales at our retail stores, we transmit
confidential credit and debit card information securely over public networks. Third parties may have the technology or know-how to breach the security of this customer information, and our security measures may not effectively prohibit others from
obtaining improper access to this information. If a person is able to circumvent our security measures, he or she could destroy or steal valuable information or disrupt our operations. Any security breach could expose us to risks of data loss,
litigation and liability and could seriously disrupt our operations and any resulting negative publicity could significantly harm our reputation.

Our ability to successfully expand our retail franchising business will depend on our ability to establish brand
equity through the use of our current and future trademarks, service marks, trade dress and other proprietary intellectual property, including our name and logos. Some or all of these intellectual property rights may not be enforceable, even if
registered, against any prior users of similar intellectual property or our competitors who seek to use similar intellectual property in areas where we operate or intend to conduct operations. If we fail to enforce any of our intellectual property
rights, then we may be unable to capitalize on our efforts to establish brand equity.

We could encounter claims from prior
users of similar intellectual property in areas where we operate or intend to conduct operations, which could result in additional expenditures and divert our managements time and attention from our operations. Conversely, competing
businesses, including any of our former retail store franchisees, could infringe on our intellectual property, which would necessarily require us to defend our intellectual property possibly at a significant cost to us.

Our retail business is vulnerable to changes in consumer preferences, economic conditions and other trends and factors that could harm our
business, results of operations, financial condition or cash flows.

Our retail business is affected by consumer
preferences, national, regional and local economic conditions, demographic trends and consumer confidence in the economy. Factors such as traffic patterns, weather conditions, local demographics and the number and locations of competing retail
service stations and convenience stores also affect the performance of our retail stores. In addition, we cannot ensure that our retail customers will continue to frequent our retail stores or that we will be able to find new retail store
franchisees or encourage our existing retail store franchisees to grow their franchised business or renew their franchise rights. Adverse changes in any of these trends or factors could reduce our retail customer traffic or sales, or impose limits
on our pricing, which could adversely affect our business, results of operations, financial condition or cash flows and, as a result, our ability to make distributions.

We face the risk of litigation in connection with our retail operations.

We are from time to time the subject of complaints or litigation from our consumers alleging illness, injury or other health or operational concerns. Adverse publicity resulting from these allegations may
materially adversely affect us and our brand, regardless of whether the allegations are valid or whether we are liable. In addition, employee claims against us based on, among other things, discrimination, harassment or wrongful termination, or
labor code violations may divert financial and management resources that would otherwise be used to benefit our future performance. There is also a risk of litigation from our franchisees. We have been subject to a variety of these and other claims
from time to time and a significant increase in the number of these claims or the number that are successful could materially adversely affect our business, prospects, financial condition, operating results or cash flows and, as a result, our
ability to make distributions.

Failure of our retail business to comply with state and local laws regulating the sale of alcohol and
tobacco products could result in the loss of necessary licenses and the imposition of fines and penalties on us, which could have a material adverse effect on our business, liquidity and results of operations.

State and local laws regulate the sale of alcohol and tobacco products. In certain areas where our stores are located, state or local laws
limit the hours of operation for the sale of alcohol, or prohibit the sale of alcohol, and permit the sale of alcohol and tobacco products only to persons older than a certain age. State and local regulatory agencies have the authority to approve,
revoke, suspend or deny applications for, and renewals of, permits and licenses relating to the sale of alcohol and tobacco products and to issue fines to stores for the improper sale of alcohol and tobacco products. Most jurisdictions, in their
permit and license applications, require an applicant to disclose past denials, suspensions, or revocations of permits or licenses relating to the sale of alcohol and tobacco products in any jurisdiction. Thus, if we experience a denial, suspension,
or revocation in one jurisdiction, then it could have an adverse effect on our ability to obtain permits and licenses relating to the sale of alcohol and tobacco products in other jurisdictions. In addition, the failure of our retail business to
comply with state and local laws regulating the sale of alcohol and tobacco products could result in the loss of necessary licenses and the imposition of fines and penalties on us. Such a loss or imposition could have a material adverse effect on
our business, liquidity and results of operations and, as a result, our ability to make distributions.

Risks Related to an Investment in
Us

The board of directors of our general partner adopted a policy to distribute an amount equal to the available cash we generate
each quarter, which could limit our ability to grow and make acquisitions.

The board of directors of our general
partner adopted a policy to distribute an amount equal to the available cash we generate each quarter to our unitholders. As a result, we will rely primarily upon external financing sources, including commercial bank borrowings and the issuance of
debt and equity securities, to fund our acquisitions and expansion capital expenditures. As such, to the extent we are unable to finance growth externally, our distribution policy will significantly impair our ability to grow.

In addition, because of our distribution policy, our growth, if any, may not be as robust as that of businesses that reinvest their
available cash to expand ongoing operations. To the extent we issue additional units in connection with any acquisitions or expansion capital expenditures or as in-kind distributions, current unitholders will experience dilution and the payment of
distributions on those additional units will decrease the amount we distribute on each outstanding unit. There are no limitations in our partnership agreement on our ability to issue additional units, including units ranking senior to the common
units. The incurrence of additional commercial borrowings or other debt to finance our growth strategy would result in increased interest expense, which, in turn, would reduce the available cash that we have to distribute to our unitholders. See
Managements Discussion and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesOur Distribution Policy.

Our general partner, the indirect owners of which include ACON Refining, TPG Refining and entities in which our President and Chief Executive Officer holds an interest, has fiduciary duties to its
owners, and the interests of ACON Refining, TPG Refining and entities in which our President and Chief Executive Officer holds an interest may differ significantly from, or conflict with, the interests of our public unitholders.

Our general partner is responsible for managing us. Although our general partner has fiduciary duties to manage us in a manner that it
believes is in our best interests, the fiduciary duties are specifically limited by the express terms of our partnership agreement, and the directors and officers of our general partner also have fiduciary duties to manage our general partner in a
manner beneficial to its owners, which include ACON Refining, TPG Refining and Mr. Kuchta. The interests of ACON Refining, TPG Refining and Mr. Kuchta may differ from, or conflict with, the interests of our unitholders. In resolving these conflicts,
our general partner may favor its own interests or the interests of its owners over our interests and those of our unitholders.

The potential conflicts of interest include, among others, the following:



Neither our partnership agreement nor any other agreement will require the owners of our general partner to pursue a business strategy that favors us.
The affiliates of our general partner have fiduciary duties to make decisions in their own best interests and in the best interest of their owners, which may be contrary to our interests. In addition, our general partner is allowed to take into
account the interests of parties other than us or our unitholders, such as its owners, in resolving conflicts of interest, which has the effect of limiting its fiduciary duty to our unitholders.



Our general partner has limited its liability and reduced its fiduciary duties under our partnership agreement and has also restricted the remedies
available to our unitholders for actions that, without those limitations and reductions, might constitute breaches of fiduciary duty. As a result of purchasing common units, unitholders consent to some actions and conflicts of interest that might
otherwise constitute a breach of fiduciary or other duties under applicable state law.



The board of directors of our general partner will determine the amount and timing of asset purchases and sales, capital expenditures, borrowings,
repayment of indebtedness and issuances of additional partnership interests, each of which can affect the amount of cash that is available for distribution to our unitholders.



Our partnership agreement does not restrict our general partner from causing us to pay it or its affiliates for any services rendered to us or entering
into additional contractual arrangements with any of these entities on our behalf. There is no limitation in our partnership agreement on the amounts our general partner can cause us to pay it or its affiliates.



Our general partner may exercise its rights to call and purchase all of our common units if at any time it and its affiliates own more than 90% of the
units.



Our general partner will control the enforcement of obligations owed to us by it and its affiliates. In addition, our general partner will decide
whether to retain separate counsel or others to perform services for us.



Our general partner determines which costs incurred by it and its affiliates are reimbursable by us.

See Conflicts of Interest and Fiduciary Duties.

Our partnership agreement limits the liability and reduces the fiduciary duties of our general partner and restricts the remedies available to us and our common unitholders for actions taken by our
general partner that might otherwise constitute breaches of fiduciary duty.

Our partnership agreement limits the
liability and reduces the fiduciary duties of our general partner, while also restricting the remedies available to our common unitholders for actions that, without these limitations and reductions, might constitute breaches of fiduciary duty.
Delaware partnership law permits such contractual reductions of fiduciary duty. By purchasing common units, common unitholders consent to some actions that might otherwise constitute a breach of fiduciary or other duties applicable under state law.
Our partnership agreement contains provisions that reduce the standards to which our general partner would otherwise be held by state fiduciary duty law. For example:



Our partnership agreement permits our general partner to make a number of decisions in its individual capacity, as opposed to its capacity as general
partner. This entitles our general partner to consider only the interests and factors that it desires, and it has no duty or obligation to give any consideration to any interest of, or factors affecting, our common unitholders. Decisions made by our
general partner in its individual capacity will be made by its owners and not by the board of directors of our general partner. Examples include the exercise of the general partners call right, its voting rights with respect to any common
units it may own and its determination whether or not to consent to any merger or consolidation or amendment to our partnership agreement.

Our partnership agreement provides that our general partner will not have any liability to us or our unitholders for decisions made in its capacity as
general partner so long as it acted in good faith, meaning it believed that the decisions were not adverse to the interests of our partnership.



Our partnership agreement provides that our general partner and the officers and directors of our general partner will not be liable for monetary
damages to us for any acts or omissions unless there has been a final and non-appealable judgment entered by a court of competent jurisdiction determining that our general partner or those persons acted in bad faith or, in the case of a criminal
matter, acted with knowledge that such persons conduct was unlawful.



Our partnership agreement provides that our general partner will not be in breach of its obligations under the partnership agreement or its duties to
us or our limited partners if a transaction with an affiliate or the resolution of a conflict of interest is:



Approved by the conflicts committee of the board of directors of our general partner, although our general partner is not obligated to seek such
approval; or



Approved by the vote of a majority of the outstanding units, excluding any units owned by our general partner and its affiliates.

In connection with a situation involving a transaction with an affiliate or a conflict of interest, any
determination by our general partner must be made in good faith. If an affiliate transaction or the resolution of a conflict of interest is not approved by our unitholders or the conflicts committee then it will be presumed that, in making its
decision, taking any action or failing to act, the board of directors acted in good faith, and in any proceeding brought by or on behalf of any limited partner or the partnership, the person bringing or prosecuting such proceeding will have the
burden of overcoming such presumption. See Conflicts of Interest and Fiduciary Duties.

Our partnership agreement
provides that a conflicts committee may be comprised of one or more directors. If we establish a conflicts committee with only one director, your interests may not be as well served as if we had a conflicts committee comprised of at least two
independent directors.

By purchasing a common unit, a unitholder will become bound by the provisions of our partnership
agreement, including the provisions described above. See Description of Our Common UnitsTransfer of Common Units.

Northern Tier Holdings has the power to appoint and remove our general partners directors.

Northern Tier Holdings has the power to elect all of the members of the board of directors of our general partner. Our general partner has
control over all decisions related to our operations. See ManagementOur Management. Our public unitholders do not have an ability to influence any operating decisions and will not be able to prevent us from entering into any
transactions. Furthermore, the goals and objectives of the owners of our general partner may not be consistent with those of our public unitholders.

Common units are subject to our general partners call right.

If at any time our general partner and its affiliates own more than 90% of our outstanding common units, our general partner will have the
right, which it may assign to any of its affiliates or to us, but not the obligation, to acquire all, but not less than all, of the units held by unaffiliated unitholders at a price not less than their then-current market price, as calculated
pursuant to the terms of our partnership agreement. As a result, you may be required to sell your units at an undesirable time or price and may not receive any return on your investment. You may also incur a tax liability upon a sale of your units.
Our general partner is not obligated to obtain a fairness opinion regarding the value of the units to be repurchased by it upon exercise of the call right. There is no restriction in our partnership agreement that prevents our general partner from
issuing additional units and then exercising its call right. Our general partner may use its own discretion, free of fiduciary duty restrictions, in determining whether to exercise this right. See The Partnership AgreementCall
Right.

Our unitholders have limited voting rights and are not entitled to elect our general partner or our
general partners directors.

Unlike the holders of common stock in a corporation, our unitholders have only
limited voting rights on matters affecting our business and, therefore, limited ability to influence managements decisions regarding our business. Unitholders will have no right to elect our general partner or our general partners board
of directors on an annual or other continuing basis. The board of directors of our general partner, including the independent directors, will be chosen entirely by Northern Tier Holdings as the direct owner of the general partner and not by our
common unitholders. Unlike publicly traded corporations, we will not hold annual meetings of our unitholders to elect directors or conduct other matters routinely conducted at annual meetings of stockholders. Furthermore, even if our unitholders are
dissatisfied with the performance of our general partner, they will have no practical ability to remove our general partner. These limitations could adversely affect the price at which the common units will trade.

Our public unitholders will not have sufficient voting power to remove our general partner without Northern Tier Holdings consent.

Our general partner may only be removed by a vote of the holders of at least two-thirds of the outstanding units,
including any units owned by our general partner and its affiliates (including Northern Tier Holdings). Following the closing of this offering, Northern Tier Holdings will own approximately 69.9% of our common units (or approximately 68.4% of our
common units if the underwriters exercise their option to purchase additional common units in full), which means holders of common units purchased in this offering will not be able to remove the general partner without the consent of Northern Tier
Holdings.

Our partnership agreement restricts the voting rights of unitholders owning 20% or more of our common units (other than
our general partner and its affiliates and permitted transferees).

Our partnership agreement restricts
unitholders voting rights by providing that any units held by a person that owns 20% or more of any class of units then outstanding, other than our general partner, its affiliates, their transferees and persons who acquired such units with the
prior approval of the board of directors of our general partner, may not vote on any matter. Our partnership agreement also contains provisions limiting the ability of common unitholders to call meetings or to acquire information about our
operations, as well as other provisions limiting the ability of our common unitholders to influence the manner or direction of management.

Cost reimbursements due to our general partner and its affiliates will reduce cash available for distribution to you.

Prior to making any distribution on our outstanding units, we will reimburse our general partner for all expenses it incurs on our behalf
including, without limitation, salary, bonus, incentive compensation and other amounts paid to its employees and executive officers who perform services for us. There are no limits contained in our partnership agreement on the amounts or types of
expenses for which our general partner and its affiliates may be reimbursed. The payment of these amounts, including allocated overhead, to our general partner and its affiliates could adversely affect our ability to make distributions to our
unitholders. See Managements Discussion and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesOur Distribution Policy, Certain Relationships and Related Person
Transactions and Conflicts of Interest and Fiduciary DutiesConflicts of Interest.

Unitholders may have
liability to repay distributions.

In the event that: (1) we make distributions to our unitholders when our
nonrecourse liabilities exceed the sum of (a) the fair market value of our assets not subject to recourse liability and (b) the excess of the fair market value of our assets subject to recourse liability over such liability, or a
distribution causes such a result, and (2) a unitholder knows at the time of the distribution of such circumstances, such unitholder will be liable for a period

of three years from the time of the impermissible distribution to repay the distribution under Section 17-607 of the Delaware Revised Uniform Limited Partnership Act (the Delaware
Act).

Likewise, upon the winding up of the partnership, in the event that (1) we do not distribute assets in the
following order: (a) to creditors in satisfaction of their liabilities; (b) to partners and former partners in satisfaction of liabilities for distributions owed under our partnership agreement; (c) to partners for the return of their
contribution; and finally (d) to the partners in the proportions in which the partners share in distributions and (2) a unitholder knows at the time of such circumstances, then such unitholder will be liable for a period of three years
from the impermissible distribution to repay the distribution under Section 17-804 of the Delaware Act.

A purchaser of
common units who becomes a limited partner is liable for the obligations of the transferring limited partner to make contributions to us that are known by the purchaser at the time it became a limited partner and for unknown obligations if the
liabilities could be determined from our partnership agreement.

Our general partners interest in us and the control of our
general partner may be transferred to a third party without unitholder consent.

Our general partner may transfer its
general partner interest in us to a third party without the consent of the unitholders. Furthermore, there is no restriction in our partnership agreement on the ability of the owners of our general partner to transfer their equity interests in our
general partner to a third party. The new equity owner of our general partner would then be in a position to replace the board of directors and the officers of our general partner with its own choices and to influence the decisions taken by the
board of directors and officers of our general partner.

If our unit price fluctuates after this offering, you could lose a significant
part of your investment.

The market price of our common units may be influenced by many factors including:

the amount of distributions we make and our earnings or those of other companies in our industry or other publicly traded partnerships;



strategic actions by our competitors;



changes in revenue or earnings estimates, or changes in recommendations or withdrawal of research coverage, by equity research analysts;



speculation in the press or investment community;



sales of our common units by us or other unitholders, or the perception that such sales may occur;



changes in accounting principles;



additions or departures of key management personnel;



actions by our unitholders;



general market conditions, including fluctuations in commodity prices; and



domestic and international economic, legal and regulatory factors unrelated to our performance.

As a result of these factors, investors in our common units may not be able to resell their common units at or above the offering price.
In addition, the stock market in general has experienced extreme price and volume fluctuations that have often been unrelated or disproportionate to the operating performance of companies like us. These broad market and industry factors may
materially reduce the market price of our common units, regardless of our operating performance.

Our new standalone finance and accounting information systems may fail to operate effectively or as
intended, which could adversely affect the reliability of our financial statements.

Pursuant to a transition services
agreement, Marathon agreed to provide us with, among other things, administrative and support services, including finance, accounting and information system services, for up to 18 months following the closing of the Marathon Acquisition to allow us
time to build the infrastructure required to operate these functions independently. During the fourth quarter of 2011, we transitioned the finance, accounting information system services and functions from Marathon to our own standalone information
systems and processes. It is possible that we will discover material shortcomings in our new standalone finance accounting information systems and processes, including those that may represent material weaknesses in our internal control over
financial reporting, that are not currently known to us. Any such defects could adversely affect the reliability of our financial statements.

If we are unable to satisfy the requirements of Section 404 of the Sarbanes-Oxley Act, or our internal control over financial reporting is not
effective, the reliability of our financial statements may be questioned, and our unit price may suffer.

Section 404 of the Sarbanes-Oxley Act requires any company subject to the reporting requirements of the U.S. securities laws to
perform a comprehensive evaluation of its and its subsidiaries internal controls. To comply with these requirements, we will be required to document and test our internal control procedures, our management will be required to assess and issue
a report concerning our internal control over financial reporting, and, under the Sarbanes-Oxley Act, our independent auditors will be required to issue an opinion on managements assessment and the effectiveness of our internal control over
financial reporting. Our compliance with Section 404 of the Sarbanes-Oxley Act will first be reported on in connection with the filing of our second Annual Report on Form 10-K. The rules governing the standards that must be met for management
to assess our internal control over financial reporting are complex and require significant documentation, testing and possible remediation. During the course of its testing, our management may identify material weaknesses, which may not be remedied
in time to meet the deadline imposed by the SEC rules implementing Section 404. If our management cannot favorably assess the effectiveness of our internal control over financial reporting, or our auditors identify material weaknesses in our
internal control, investor confidence in our financial results may weaken, and the price of our common units may suffer.

We may issue
additional common units and other equity interests without your approval, which would dilute your existing ownership interests.

Under our partnership agreement, we are authorized to issue an unlimited number of additional interests without a vote of the unitholders. The issuance by us of additional common units or other equity
interests of equal or senior rank will have the following effects:



the proportionate ownership interest of unitholders immediately prior to the issuance will decrease;



the amount of cash distributions on each unit will decrease;



the ratio of our taxable income to distributions may increase;



the relative voting strength of each previously outstanding unit will be diminished; and



the market price of the common units may decline.

In addition, our partnership agreement does not prohibit the issuance of equity interests by our subsidiary, which may effectively rank senior to the common units.

Units eligible for future sale may cause the price of our common units to decline.

Sales of substantial amounts of our common units in the public market, or the perception that these sales may occur, could cause the
market price of our common units to decline. This could also impair our ability to raise additional capital through the sale of our equity interests.

As of January 9, 2013, there were 91,921,112 units outstanding. 18,687,500 common units were
sold to the public in our initial public offering and an aggregate of 73,227,500 common units are owned by Northern Tier Holdings. The common units sold in our initial public offering, as well as the units to be sold in this offering, will be freely
transferable without restriction or further registration under the Securities Act of 1933, as amended (the Securities Act), by persons other than affiliates, as that term is defined in Rule 144 under the Securities Act.

In addition, we are party to a registration rights agreement with Northern Tier Holdings LLC and certain of its indirect
owners pursuant to which we may be required to register the sale of the units they hold under the Securities Act and applicable state securities laws.

We will incur increased costs as a result of being a publicly traded partnership.

As a publicly traded partnership, we will incur significant legal, accounting and other expenses that we did not incur prior to our initial public offering. In addition, the Sarbanes-Oxley Act and the
Dodd-Frank Act, as well as rules implemented by the SEC and the NYSE, require, or will require, publicly traded entities to adopt various corporate governance practices that will further increase our costs. Before we are able to pay distributions to
our unitholders, we must first pay our expenses, including the costs of being a public company and other operating expenses. As a result, the amount of cash we have available for distribution to our unitholders will be affected by our expenses,
including the costs associated with being a publicly traded partnership. We estimate that we will incur approximately $3.5 million of estimated incremental costs per year, some of which will be direct charges associated with being a publicly traded
partnership and some of which will be allocated to us by our general partner and its affiliates; however, it is possible that our actual incremental costs of being a publicly traded partnership will be higher than we currently estimate.

Prior to our initial public offering, we have not filed reports with the SEC. Following our initial public offering, we became subject to
the public reporting requirements of the Securities Exchange Act of 1934, as amended (the Exchange Act). We expect these requirements will increase our legal and financial compliance costs and make compliance activities more
time-consuming and costly. For example, as a result of becoming a publicly traded partnership, we are required to have at least three independent directors and adopt policies regarding internal controls and disclosure controls and procedures,
including the preparation of reports on internal control over financial reporting. In addition, we will incur additional costs associated with our publicly traded company reporting requirements.

As a publicly traded limited partnership we qualify for, and will rely on, certain exemptions from the New York Stock Exchanges
corporate governance requirements.

As a publicly traded partnership, we qualify for, and will rely on, certain
exemptions from the NYSEs corporate governance requirements, including:



the requirement that a majority of the board of directors of our general partner consist of independent directors;



the requirement that the board of directors of our general partner have a nominating/corporate governance committee that is composed entirely of
independent directors; and



the requirement that the board of directors of our general partner have a compensation committee that is composed entirely of independent directors.

As a result of these exemptions, our general partners board of directors will not be comprised of a
majority of independent directors, our general partners compensation committee may not be comprised entirely of independent directors. Accordingly, unitholders will not have the same protections afforded to equityholders of companies that are
subject to all of the corporate governance requirements of the NYSE. See Management.

In addition to reading the following risk factors, you should read Material Federal Income Tax Consequences for a more complete discussion of the expected material federal income tax
consequences of owning and disposing of common units.

Our tax treatment depends on our status as a partnership for federal income tax
purposes, as well as our not being subject to a material amount of entity-level taxation by individual states. If the IRS were to treat us as a corporation for federal income tax purposes, or we were to become subject to material additional amounts
of entity-level taxation for state tax purposes, then our cash available for distribution to you could be substantially reduced.

The anticipated after-tax economic benefit of an investment in our common units depends largely on our being treated as a partnership for federal income tax purposes. We have not requested, and do not
plan to request, a ruling from the Internal Revenue Service (the IRS) on this or any other tax matter affecting us. To maintain our status as a partnership for federal income tax purposes, current law requires that 90% or more of our
gross income for every taxable year consist of qualifying income, as defined in Section 7704 of the Internal Revenue Code of 1986, as amended (the Code). Qualifying income includes (i) income and gains
derived from the refining, transportation, processing and marketing of crude oil, natural gas and products thereof, (ii) interest (other than from a financial business), (iii) dividends, (iv) gains from the sale of real property and
(v) gains from the sale or other disposition of capital assets held for the production of qualifying income.

Despite the
fact that we are organized as a limited partnership under Delaware law, it is possible in certain circumstances for a partnership such as ours to be treated as a corporation for federal income tax purposes. Although we do not believe, based upon our
current operations, that we will be so treated, a change in our business (or a change in current law) could cause us to be treated as a corporation for federal income tax purposes or otherwise subject us to taxation as an entity.

If we were treated as a corporation for federal income tax purposes, we would pay federal income tax on our taxable income at the
corporate tax rate, which is currently a maximum of 35% and would likely pay state income tax at varying rates. Distributions to you would generally be taxed again as corporate distributions, and no income, gains, losses, deductions or credits would
flow through to you. Because a tax would be imposed upon us as a corporation, our cash available for distribution to you would be substantially reduced. Therefore, treatment of us as a corporation would result in a material reduction in the
anticipated cash flow and after-tax return to our unitholders, likely causing a substantial reduction in the value of our common units.

The tax treatment of publicly traded partnerships or an investment in our units could be subject to potential legislative, judicial or
administrative changes and differing interpretations, possibly on a retroactive basis.

The present federal income tax
treatment of publicly traded partnerships, including us, or an investment in our common units may be modified by administrative, legislative or judicial changes at any time. For example, members of Congress have recently considered substantive
changes to the existing federal income tax laws that affect publicly traded partnerships. Any modification to the federal income tax laws and interpretations thereof may be applied retroactively and could impose additional administrative
requirements on us or make it more difficult or impossible to meet the exception for certain publicly traded partnerships to be treated as partnerships for federal income tax purposes. We are unable to predict whether any of these changes, or other
proposals will be reintroduced or will ultimately be enacted. Any such changes could negatively impact the value of an investment in our common units.

You will be required to pay taxes on your share of our income even if you do not receive any cash
distributions from us.

Because our unitholders will be treated as partners to whom we will allocate taxable income
that could be different in amount than the cash we distribute, you will be required to pay any federal income taxes and, in some cases, state and local income taxes on your share of our taxable income whether or not you receive cash distributions
from us. You may not receive cash distributions from us equal to your share of our taxable income or even equal to the actual tax liability that results from that income.

The sale or exchange of 50% or more of our capital and profits interests during any twelve-month period will result in the termination of our partnership for federal income tax purposes.

We will be considered to have terminated our partnership for federal income tax purposes if there is a sale or
exchange of 50% or more of the total interests in our capital and profits within a twelve-month period. Following this offering, Northern Tier Holdings will own more than 50% of the total interests in our capital and profits. If transfers within a
twelve-month period of common units by Northern Tier Holdings, by itself or in combination with other transfers of common units, represent 50% or more of the total interests in our capital and profits, we will be considered to have terminated our
partnership for federal income tax purposes. Our termination would, among other things, result in the closing of our taxable year for all unitholders and could result in a deferral of depreciation deductions allowable in computing our taxable
income. In the case of a unitholder reporting on a taxable year other than a fiscal year ending December 31, the closing of our taxable year may also result in more than twelve months of our taxable income or loss being includable in its
taxable income for the year of termination. Our termination currently would not affect our classification as a partnership for federal income tax purposes, but instead, we would be treated as a new partnership for federal income tax purposes. If
treated as a new partnership, we must make new tax elections and could be subject to penalties if we are unable to determine that a termination occurred. See Material Federal Income Tax ConsequencesDisposition of UnitsConstructive
Termination for a discussion of the consequences of our termination for federal income tax purposes.

Tax gain or loss on the
disposition of our common units could be more or less than expected.

If you sell your common units, you will recognize
a gain or loss equal to the difference between the amount realized and your tax basis in those common units. Because distributions in excess of your allocable share of our net taxable income decrease your tax basis in your common units, the amount,
if any, of such prior excess distributions with respect to the units you sell will, in effect, become taxable income to you if you sell such units at a price greater than your tax basis in those units, even if the price you receive is less than your
original cost. Furthermore, a substantial portion of the amount realized, whether or not representing gain, may be taxed as ordinary income due to potential recapture items, including depreciation recapture. In addition, because the amount realized
includes a unitholders share of our nonrecourse liabilities, if you sell your units, you may incur a tax liability in excess of the amount of cash you receive from the sale. See Material Federal Income Tax ConsequencesDisposition
of UnitsRecognition of Gain or Loss for a further discussion of the foregoing.

Tax-exempt entities and non-U.S. persons
face unique tax issues from owning common units that may result in adverse tax consequences to them.

Investment in
common units by tax-exempt entities, such as employee benefit plans and individual retirement accounts (IRAs), and non-U.S. persons raises issues unique to them. For example, virtually all of our income allocated to organizations that
are exempt from federal income tax, including IRAs and other retirement plans, will be unrelated business taxable income and will be taxable to them. Distributions to non-U.S. persons will be reduced by withholding taxes at the highest applicable
effective tax rate, and non-U.S. persons will be required to file federal tax returns and pay tax on their share of our taxable income. If you are a tax-exempt entity or a non-U.S. person, you should consult your tax advisor before investing in our
common units.

If the IRS contests the federal income tax positions we take, the market for our common units may be
adversely impacted and the cost of any IRS contest will reduce our cash available for distribution to you.

The IRS may
adopt positions that differ from the positions we take. It may be necessary to resort to administrative or court proceedings to sustain some or all of the positions we take. A court may not agree with some or all of the positions we take. Any
contest with the IRS may materially and adversely impact the market for our common units and the price at which they trade. Our costs of any contest with the IRS will be borne indirectly by our unitholders because the costs will reduce our cash
available for distribution.

We will treat each purchaser of our common units as having the same tax benefits without regard to the
actual common units purchased. The IRS may challenge this treatment, which could adversely affect the value of the common units.

Because we cannot match transferors and transferees of common units, we will adopt depreciation and amortization positions that may not conform to all aspects of existing and proposed U.S. Treasury
regulations (the Treasury Regulations). A successful IRS challenge to those positions could adversely affect the amount of tax benefits available to you. It also could affect the timing of these tax benefits or the amount of gain from
your sale of common units and could have a negative impact on the value of our common units or result in audit adjustments to your tax returns. See Material Federal Income Tax ConsequencesTax Consequences of Unit OwnershipSection
754 Election for a further discussion of the effect of the depreciation and amortization positions we will adopt.

We will prorate
our items of income, gain, loss and deduction between transferors and transferees of our units each month based upon the ownership of our units on the first day of each month, instead of on the basis of the date a particular unit is transferred. The
IRS may challenge this treatment, which could change the allocation of items of income, gain, loss and deduction among our unitholders.

We will prorate our items of income, gain, loss and deduction between transferors and transferees of our common units each month based upon the ownership of our common units on the first day of each
month, instead of on the basis of the date a particular common unit is transferred. The use of this proration method may not be permitted under existing Treasury Regulations, and although the U.S. Treasury Department issued proposed Treasury
Regulations allowing a similar monthly simplifying convention, such regulations are not final and do not specifically authorize the use of the proration method we have adopted. Accordingly, our counsel is unable to opine as to the validity of this
method. If the IRS were to successfully challenge our proration method, we may be required to change the allocation of items of income, gain, loss and deduction among our unitholders.

A unitholder whose common units are loaned to a short seller to cover a short sale of common units may be considered as having disposed of those common units. If so, he would no longer
be treated for tax purposes as a partner with respect to those common units during the period of the loan and may recognize gain or loss from the disposition.

Because there is no tax concept of loaning a partnership interest, a unitholder whose common units are loaned to a short seller to cover a short sale of common units may be considered as
having disposed of the loaned units. In that case, he may no longer be treated for tax purposes as a partner with respect to those common units during the period of the loan to the short seller and the unitholder may recognize gain or loss from such
disposition. Moreover, during the period of the loan to the short seller, any of our income, gain, loss or deduction with respect to those common units may not be reportable by the unitholder and any cash distributions received by the unitholder as
to those common units could be fully taxable as ordinary income. Unitholders desiring to assure their status as partners and avoid the risk of gain recognition from a loan to a short seller should modify any applicable brokerage account agreements
to prohibit their brokers from borrowing their common units. See Material Federal Income Tax ConsequencesTax Consequences of Unit OwnershipTreatment of Short Sales for a further discussion of the foregoing.

Unitholders may be subject to state and local taxes and return filing requirements in jurisdictions
where they do not live as a result of investing in our common units.

In addition to federal income taxes, unitholders
may become subject to other taxes, including state, local and non-U.S. taxes, unincorporated business taxes and estate, inheritance or intangible taxes that are imposed by jurisdictions in which we conduct business or own property in the future,
even if they do not live in any of those jurisdictions. We currently conduct business or own property in several states, each of which imposes an income tax on corporations and other entities and a personal income tax. We may own property or conduct
business in other states or non-U.S. countries in the future. Unitholders may be required to file state and local income tax returns and pay state and local income taxes in some or all of those various jurisdictions. Further, unitholders may be
subject to penalties for failure to comply with those requirements. It is the unitholders responsibility to file all federal, state, local and non-U.S. tax returns.

As part of the IPO Transactions, some of our subsidiaries elected to be treated as corporations for federal income tax purposes and became subject to corporate-level income taxes.

As part of the IPO Transactions, as described in Managements Discussion and Analysis of Financial
Condition and Results of OperationsComparability of Historical ResultsThe IPO Transactions, certain of our subsidiaries, including Northern Tier Retail Holdings LLC, which holds all of the ownership interests in Northern Tier
Retail LLC and Northern Tier Bakery LLC, and Northern Tier Energy Holdings LLC, elected to be treated as corporations for federal income tax purposes, which subjected them to corporate-level income taxes and may reduce the cash available for
distribution to us and, in turn, to unitholders. In the future, we may conduct additional operations through these subsidiaries or additional subsidiaries that are subject to corporate-level income taxes. Our historical financial statements prior to
our initial public offering do not reflect the corporate-level taxes that these subsidiaries would be required to pay in the future, which may affect the financial statements usefulness in predicting our future earnings and ability to
distribute cash. Additionally, any losses in these subsidiaries will not be available to offset income generated by our other business operations, and may necessitate additional cash contributions that would reduce the cash available for
distribution to unitholders.

This prospectus includes forward-looking statements. The words believe, expect,
anticipate, plan, intend, foresee, should, would, could, attempt, appears, forecast, outlook, estimate,
project, potential, may, will, are likely or other similar expressions are intended to identify forward-looking statements, which are generally not historical in nature. These
forward-looking statements are based on our current expectations and beliefs concerning future developments and their potential effect on us. While management believes that these forward-looking statements are reasonable as and when made, there can
be no assurance that future developments affecting us will be those that we anticipate, and any and all of our forward-looking statements in this prospectus may turn out to be inaccurate.

Forward-looking statements appear in a number of places in this prospectus, including Summary, Risk Factors,
Managements Discussion and Analysis of Financial Conditions and Results of Operations and Business, and include statements with respect to, among other things:



our ability to make distributions on the common units;



the volatile nature of our business;



the ability of our general partner to modify or revoke our distribution policy at any time;



our business strategy and prospects;



technology;



our cash flows and liquidity;



our financial strategy, budget, projections and operating results;



the amount, nature and timing of capital expenditures;



the availability and terms of capital;



competition and government regulations;



general economic conditions and trends in the refining industry;



effectiveness of our risk management activities;



our environmental liabilities;



our counterparty credit risk;



governmental regulation and taxation of the refining industry; and



developments in oil-producing and natural gas-producing countries.

Our forward-looking statements involve significant risks and uncertainties (some of which are beyond our control) and assumptions that
could cause actual results to differ materially from our historical experience and our present expectations or projections. Important factors that could cause actual results to differ materially from those in the forward-looking statements include,
but are not limited to, those summarized below:



the overall demand for hydrocarbon products, fuels and other refined products;

our access to capital to fund expansions, acquisitions and our working capital needs and our ability to obtain debt or equity financing on satisfactory
terms;



environmental liabilities or events that are not covered by an indemnity, insurance or existing reserves;



dependence on one principal supplier for merchandise;



maintenance of our credit ratings and ability to receive open credit lines from our suppliers;



the effects of competition;



continued creditworthiness of, and performance by, counterparties;



the impact of current and future laws, rulings and governmental regulations, including guidance related to the Dodd-Frank Act;



shortages or cost increases of power supplies, natural gas, materials or labor;



weather interference with business operations;



seasonal trends in the industries in which we operate;



fluctuations in the debt markets;



potential product liability claims and other litigation;



changes in economic conditions, generally, and in the markets we serve, consumer behavior, and travel and tourism trends; and



changes in our treatment as a partnership for U.S. income or state tax purposes.

These factors are not necessarily all of the important factors that could cause actual results to differ materially from those expressed
in any of our forward-looking statements. Other unknown or unpredictable factors also could have material adverse effects on our future results. Our future results will depend upon various other risks and uncertainties, including those described
elsewhere in this prospectus under the heading, Risk Factors. Readers are cautioned not to place undue reliance on forward-looking statements, which speak only as of the date hereof. We undertake no obligation to update or revise any
forward-looking statements after the date they are made, whether as a result of new information, future events or otherwise. All forward-looking statements attributable to us are qualified in their entirety by this cautionary statement.

The common units to be offered and sold using this prospectus will be offered and sold by the selling unitholder named in this
prospectus. We will not receive any proceeds from the sale of such common units.

The following table shows our cash and capitalization as of September 30, 2012:



on a historical basis; and



on a pro forma basis to reflect the issuance and sale of $275 million of the 2020 Notes and the application of the net proceeds therefrom, together
with cash on hand of $31 million, and the conversion of our PIK units into common units.

This offering will
not affect our capitalization. You should read our financial statements and notes that are contained in this prospectus for additional information.

Approximately $258 million of the 2017 Notes have been repurchased and the remainder has been satisfied and discharged pursuant to the terms of the indenture governing
the 2017 Notes. See SummaryRecent Developments2020 Notes Offering and Tender Offer.

(2)

Relates to specific properties that did not qualify for operating lease treatment under the sale leaseback of 135 SuperAmerica convenience stores with Realty Income, a
third party equity real estate investment trust.

(3)

The repurchase and satisfaction and discharge of the 2017 Notes resulted in a termination of the PIK Period, as such term is defined in our First Amended and Restated
Limited Partnership Agreement. Upon termination of the PIK Period, all of the PIK units automatically converted into common units and thereafter were entitled to receive cash distributions when and as decided by the board of directors of our general
partner, instead of distributions payable in kind in additional PIK units.

(4)

Pro forma reflects the pro forma after-tax charge from repurchase of the 2017 Notes of approximately $48 million.

Our common units are listed on the New York Stock Exchange under the symbol NTI. The last reported sales price of the
common units on January 15, 2013 was $25.46. As of January 15, 2013, we had issued and outstanding 91,921,112 common units, which were held of record by 6 unitholders. The following table sets forth the range of high and low sales prices of the
common units on the New York Stock Exchange, as well as the amount of cash distributions paid per common unit for the periods indicated.

Common Unit Price Ranges

Cash Distributionsper CommonUnit(1)

Quarter Ended

High

Low

March 31, 2013 (through January 15, 2013)(2)

$

26.50

$

24.61

December 31, 2012(3)

$

27.11

$

19.97

September 30, 2012(4) (from July 26, 2012)

$

21.27

$

13.00

$

1.48

(1)

Distributions are shown for the quarter with respect to which they were declared.

(2)

The distribution attributable to the quarter ending March 31, 2013 has not yet been declared or paid.

(3)

The distribution attributable to the quarter ending December 31, 2012 has not yet been declared or paid.

(4)

The distribution attributable to the quarter ended September 30, 2012 represents a prorated distribution for the period from the closing of our initial public
offering through September 30, 2012 and was paid on November 29, 2012 to unitholders of record as of November 21, 2012.

The following tables present certain selected historical condensed consolidated financial data. The combined financial
statements as of and for the years ended December 31, 2007, 2008 and 2009 and the eleven months ended November 30, 2010 represent a carve-out financial statement presentation of several operating units of Marathon, which we refer to as
Predecessor. For more information on the carve-out presentation, see Managements Discussion and Analysis of Financial Condition and Results of OperationsPredecessor Carve-Out Financial Statements and our financial
statements and the notes thereto included elsewhere in this prospectus. The historical financial data for periods prior to December 1, 2010 presented below do not reflect the consummation of the Marathon Acquisition and the transactions related
thereto or our capital structure following the Marathon Acquisition and the transactions related thereto. Northern Tier Energy LLC was formed on June 23, 2010 and entered into certain agreements with Marathon on October 6, 2010 to acquire
the Marathon Assets. At the closing of the Marathon Acquisition on December 1, 2010, Northern Tier Energy LLC acquired the Marathon Assets. Northern Tier Energy LLC had no operating activities between its June 23, 2010 inception date and
the closing date of the Marathon Acquisition, although it incurred various transaction and formation costs which have been included in the 2010 Successor Period. Upon the closing of our initial public offering, the historical consolidated financial
statements of Northern Tier Energy LLC became the historical consolidated financial statements of Northern Tier Energy LP.

The selected historical financial data as of September 30, 2012 and for the nine months ended September 30, 2011 and 2012 are
derived from unaudited financial statements and the notes thereto included elsewhere in this prospectus. The selected historical financial data as of December 31, 2010 and 2011, for the year ended December 31, 2009, the eleven months ended
November 30, 2010, the 2010 Successor Period and the year ended December 31, 2011 are derived from audited financial statements and the notes thereto included elsewhere in this prospectus. The selected historical combined financial data as
of December 31, 2007, 2008, 2009 and November 30, 2010 and for the years ended December 31, 2007 and 2008 are derived from audited financial statements and the notes thereto and the summary historical balance sheet data as of
June 30, 2011 is derived from unaudited financial statements and the notes thereto that are not included in this prospectus.

On a pro forma basis and adjusted for certain items to give effect to our initial public offering, the tendering of our 2017 Notes and the private placement of our 2020 Notes, net earnings for the year
ended December 31, 2011 would have been $33.1 million.

The items related to our initial public offering include a
reduction of interest expense of $3.0 million related to the redemption of a portion of the 2017 Notes, increased selling, general and administrative expenses of $3.5 million as a result of being a publicly traded partnership (resulting in pro forma
selling, general and administrative expense of $94.2 million for the year ended December 31, 2011) and a reduction of $2.1 million in management fees paid to ACON Management and TPG Management (resulting in pro forma other income of $6.6
million for the year ended December 31, 2011).

On November 8, 2012, we completed a private placement of $275
million in aggregate principal amount of the 2020 Notes. We used the net proceeds of the offering and cash on hand of $31 million (i) to repurchase our outstanding 2017 Notes that were tendered pursuant to our previously announced tender offer and
(ii) to satisfy and discharge any remaining 2017 Notes outstanding (which notes were called for redemption after the closing of the tender offer) and to pay related fees and expenses. The repurchase of the 2017 Notes resulted in an after-tax charge
of approximately $48 million in the fourth quarter of 2012. On a pro forma basis after giving effect to such private placement and tender offer, we would have recorded a reduction of approximately $8.9 million of interest expense for the year ended
December 31, 2011. The pro forma impacts of the private placement and tender offer and the pro forma impacts of the partial redemption of the 2017 Notes as part of our initial public offering would have resulted in a pro forma interest expense
of $30.2 million for the year ended December 31, 2011.

The historical financial and other data presented below are not
necessarily indicative of the results expected for any future period.

You should read these tables along with Risk Factors, Use of
Proceeds, Capitalization, Managements Discussion and Analysis of Financial Condition and Results of Operations, Business and our financial statements and the notes thereto, included elsewhere in this
prospectus.

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our financial statements and related notes included elsewhere in this
prospectus. The following discussion contains forward-looking statements that reflect our future plans, estimates, beliefs and expected performance. Our actual results may differ materially from those currently anticipated and expressed
in such forward-looking statements as a result of a number of factors, including those we discuss under Risk Factors elsewhere in this prospectus. We caution that assumptions, expectations, projections, intentions or beliefs about future
events may, and often do, vary from actual results and the differences can be material. See Cautionary Note Regarding Forward-Looking Statements.

Overview

We are an independent downstream energy limited partnership with
refining, retail and pipeline operations that serves the PADD II region of the United States. We operate our assets in two business segments: the refining business and the retail business. For the nine months ended September 30, 2012, we had
total revenues of approximately $3.4 billion, operating income of $426.8 million, net earnings of $113.1 million and Adjusted EBITDA of $577.3 million. For the year ended December 31, 2011, we had total revenues of $4.3 billion, operating
income of $422.6 million, net earnings of $28.3 million and Adjusted EBITDA of $430.7 million. For a definition, and reconciliation, of Adjusted EBITDA to net (loss) earnings, see SummarySummary Historical Condensed Consolidated
Financial and Other Data.

Refining Business

Our refining business primarily consists of a 74,000 bpd (84,500 barrels per stream day) refinery located in St. Paul Park, Minnesota. Our refinery has a Nelson complexity index of 11.5, which refers to
the number, type and capacity of processing units at the refinery. We are one of only two refineries in Minnesota and one of four refineries in the Upper Great Plains area within the PADD II region. Our refinerys complexity allows us to
process a variety of light, heavy, sweet and sour crudes, many of which have historically priced at a discount to the NYMEX WTI price benchmark, meaning we can process lower cost crude oils into higher value refined products. The PADD II region
covers Illinois, Indiana, Iowa, Kansas, Kentucky, Michigan, Minnesota, Missouri, Nebraska, North Dakota, South Dakota, Ohio, Oklahoma, Tennessee and Wisconsin. Our strategic location allows us direct access, primarily via the Minnesota Pipeline, to
sources of crude oil from Western Canada and North Dakota, as well as the ability to distribute our refined products throughout the midwestern United States. Our refinery produces a broad slate of refined products including gasoline, diesel, jet
fuel and asphalt, which are then marketed to resellers and consumers primarily in the PADD II region. Approximately 80% and 79% of our total refinery production for the nine months ended September 30, 2012 and the year ended December 31,
2011, respectively, was comprised of higher value, light refined products, including gasoline and distillates. Our refinery utilization rates, using standard industry methodologies for utilization measurement, have been 72%, 75% and 78% for the
period from inception to December 31, 2010, for the year ended December 31, 2011 and for the nine months ended September 30, 2012, respectively.

We also own various storage and transportation assets, including a light products terminal, a heavy products terminal, storage tanks, rail loading/unloading facilities and a Mississippi river dock.
Approximately 82% and 83% of our gasoline and diesel volumes for the nine months ended September 30, 2012 and the year ended December 31, 2011, respectively, were sold via our light products terminal located at the refinery to our
company-operated and franchised SuperAmerica branded convenience stores, Marathon branded convenience stores and other resellers. We have a contract with Marathon to supply substantially all of the gasoline and diesel requirements for 90
independently owned and operated Marathon branded convenience stores.

Our refining business also includes our 17% interest in the Minnesota Pipe Line Company and
MPL Investments, which owns and operates the Minnesota Pipeline, a 455,000 bpd crude oil pipeline system that transports crude oil (primarily from Western Canada and North Dakota) for approximately 300 miles from the Enbridge pipeline hub at
Clearbrook, Minnesota to our refinery. The Minnesota Pipeline has historically transported the majority of the crude oil used and processed in our refinery.

Retail Business

As of September 30, 2012, our retail business
operated 166 convenience stores under the SuperAmerica brand and also supported 68 franchised convenience stores, which are also operated under the SuperAmerica brand. These convenience stores are located primarily in Minnesota and Wisconsin and
sell various grades of gasoline and diesel, tobacco products and immediately consumable items such as non-alcoholic beverages, beer, prepared food and a large variety of snacks and prepackaged items. Our refinery supplied substantially all of the
gasoline and diesel sold in our company-operated and franchised convenience stores for the nine months ended September 30, 2012 and the year ended December 31, 2011.

We also own and operate SuperMoms Bakery, which prepares and distributes baked goods and other prepared food items for sale in our company-operated and franchised convenience stores and other third
party locations.

Outlook

Transportation fuels demand in the Upper Great Plains of the PADD II region currently exceeds supply from local refineries. Therefore, demand is fulfilled by products that are imported into the region
mostly via pipeline from other parts of the Midwest, the Rocky Mountains and the U.S. Gulf Coast. Overall refined product demand declined in 2008 as a result of prevailing economic conditions and began to improve in the first quarter of 2010. While
there continues to be a significant global macroeconomic risk that may affect the pace of growth in the United States, we have experienced continued strong overall product demand in our geographic area of operations.

Our operating performance has benefited from the widening of the price relationship between the traditional crude oil pricing benchmark,
NYMEX WTI, and the international waterborne crude oil pricing benchmark, Brent. We purchase crude oil which is priced based off NYMEX WTI. Refined products prices are set by global markets and are typically priced off Brent. Therefore, we have
enjoyed a benefit during the year ended December 31, 2011 and the nine months ended September 30, 2012 from the overall widening of the price differential between our cost of crude oil and the price of the products we sell. The widening
differential may have been attributable to several factors, including geopolitical events in the Middle East, the suspension of crude oil exports from Libya, new U.N. sanctions on Irans oil exports, and limited pipeline and other
infrastructure to transport crude oil from Cushing, Oklahoma, where NYMEX WTI is settled, to alternative markets. Please see Risk FactorsRisks Primarily Related to Our Refining BusinessOur results of operations are affected by
crude oil differentials, which may fluctuate substantially.

Predecessor Carve-Out Financial Statements

As described in the financial statements and notes thereto included elsewhere in this prospectus, this prospectus includes financial
statements for the year ended December 31, 2009 and the eleven months ended November 30, 2010 for the St. Paul Park Refinery and Retail Marketing Business, representing a carve-out financial statement presentation of several operating
units of Marathon (the Predecessor Financial Statements). All significant intercompany accounts and transactions have been eliminated in the Predecessor Financial Statements.

The Predecessor Financial Statements were prepared to reflect the way we have operated our business subsequent to the Marathon
Acquisition, which is in two segments: the refining segment and the retail segment. Except for certain assets that were not acquired (e.g., cash other than in-store cash at our convenience stores,

receivables and assets sold to third parties pursuant to a sale-leaseback arrangement between us, Speedway SuperAmerica LLC, an affiliate of Marathon, and Realty Income, a third party equity real
estate investment trust, and a crude oil supply and logistics purchase agreement with JPM CCC) and certain liabilities (e.g., accounts payable, payroll and benefits payable and deferred taxes) that were not assumed in connection with the Marathon
Acquisition, the Predecessor Financial Statements represent the Marathon Assets. In addition, the Predecessor Financial Statements include allocations of selling, general and administrative costs and other overhead costs of Marathon Oil and its
affiliates that are attributable to the operations of the Marathon Assets. We believe the assumptions, allocations and methodologies underlying the Predecessor Financial Statements are reasonable. However, the Predecessor Financial Statements do not
include all of the actual expenses that would have been incurred had the Marathon Assets been operated on a standalone basis during the periods presented and do not reflect the Marathon Assets combined results of operations, financial position
and cash flows had it been operated on a standalone basis during the periods presented.

Comparability of Historical Results

Marathon Acquisition and Related Transactions

We commenced operations in December 2010 through the acquisition of our St. Paul Park, Minnesota refinery, a 17% interest in the Minnesota Pipe Line Company and in MPL Investments, our convenience stores
and related assets from Marathon for $554 million, which included cash and the issuance to Marathon of $80 million of a noncontrolling preferred membership interest in Northern Tier Holdings LLC.

Prior to the Marathon Acquisition, the business was operated as several operating units of Marathon, and participated in Marathons
centralized cash management programs. All cash receipts were remitted to and all cash disbursements were funded by Marathon. Following the Marathon Acquisition, we operate as a standalone company, and our results of operations may not be comparable
to the historical results of operations for the periods presented, primarily for the reasons described below:



In connection with the Marathon Acquisition, we entered into a contingent consideration and margin support arrangements with Marathon under which we
could have received margin support payments of up to $60 million from MPC or could have paid MPC net earn-out payments of up to $125 million over the term of the arrangements, depending on our Adjusted EBITDA as defined in the arrangements. On
May 4, 2012, we entered into a settlement agreement with Marathon under which Marathon received $40 million of the net proceeds from our initial public offering, and Northern Tier Holdings LLC redeemed Marathons existing preferred
interest with a portion of the net proceeds from our initial public offering and issued Marathon a new $45 million preferred interest in Northern Tier Holdings LLC in consideration for relinquishing all claims with respect to earn-out payments under
the contingent consideration agreement. We also agreed, pursuant to the settlement agreement, to relinquish all claims to margin support payments under the contingent consideration agreement.



In connection with the Marathon Acquisition, certain additional transactions were consummated, and we entered into certain agreements with respect to
our operations, including the following:



2017 Notes. We issued $290 million of the 10.5% senior secured notes due December 1, 2017. The net proceeds from the sale of the
2017 Notes were used to fund part of the Marathon Acquisition. On November 14, 2012, we completed a tender offer for the 2017 Notes. See SummaryRecent Developments2020 Notes Offering and Tender Offer.



Asset-Based Revolving Credit Facility. We entered into a $300 million senior secured asset-based revolving credit facility, which is
subject to a borrowing base. We did not draw on the revolving credit facility to fund the Marathon Acquisition, other than to the extent utilized through the issuance of letters of credit. The revolving credit facility, as subsequently amended, is
available through July 17, 2017. See Managements Discussion and Analysis of Financial Condition and Results of OperationsLiquidity and Capital ResourcesDescription of Our IndebtednessSenior Secured Asset-Based
Revolving Credit Facility.

Sale-Leaseback Arrangement. Marathon sold certain real property interests, including the land underlying 135 of the SuperAmerica
convenience stores associated with our retail business and SuperMoms Bakery, to Realty Income, a third party equity real estate investment trust. In connection with the closing of the Marathon Acquisition, Realty Income leased those properties
to us on a long-term basis.



Crude Oil Inventory Purchase Agreement. JPM CCC purchased substantially all of the crude oil inventory associated with operations of
the refinery directly from Marathon pursuant to an inventory purchase agreement with Marathon.



Crude Oil Supply and Logistics Agreement. In December 2010, we entered into a crude oil supply and logistics agreement with JPM CCC,
which agreement was amended and restated in March 2012. JPM CCC assists us in the purchase of the crude oil requirements of our refinery and provides transportation and other logistical services for delivery of the crude oil to our storage tanks at
Cottage Grove, Minnesota, which are approximately two miles from our refinery. We pay the price of the crude oil plus certain agreed fees and expenses. We believe this crude oil supply and logistics agreement significantly reduces our need to
maintain crude oil inventories and allows us to take title to and price our crude oil at the refinery, as opposed to the crude oil origination point, reducing the time we are exposed to market fluctuations before the finished product output is sold.
For more information, see BusinessCrude Oil Supply.



Transition Services Agreement. Marathon agreed to provide us with administrative and support services pursuant to a transition
services agreement, including finance and accounting, human resources and information systems services, as well as support services in connection with our transition from being a part of Marathons systems and infrastructure to having our own
systems and infrastructure. Marathon is no longer providing any transition services under the agreement.



The Marathon Acquisition has been accounted for under the purchase method of accounting for business combinations which requires that the assets
acquired and liabilities assumed be adjusted to their estimated fair value at the date of the acquisition. This treatment changed the accounting basis for the assets acquired and liabilities assumed from Marathon as of December 1, 2010.



In October 2010, at our request, Marathon initiated a crack spread derivative strategy to mitigate refining margin risk on a portion of the
businesss 2011 and 2012 projected refinery production. In connection with the Marathon Acquisition, we assumed all corresponding rights and obligations for derivative instruments executed pursuant to this strategy. We incurred $301.8 million
and $310.3 million of realized losses and $32.6 million of unrealized gains and $41.9 million of unrealized losses for the nine months ended September 30, 2012 and the year ended December 31, 2011, respectively, related to these
derivative activities.

The IPO Transactions

Our results of operations for periods subsequent to the closing of our initial public offering may not be comparable to our results of
operations for periods prior to the closing of our initial public offering as a result of certain aspects of our initial public offering, including the following:



We expect that our general and administrative expenses will increase as a result of our initial public offering. Specifically, we will incur certain
expenses relating to being a publicly traded partnership, including the Exchange Act reporting expenses; expenses associated with Sarbanes-Oxley Act compliance; expenses associated with the listing of the NYSE; independent auditors fees expenses
associated with tax return and Schedule K-1 preparation and distribution; legal fees, investor relations expenses; transfer agent fees; director and officer liability insurance costs; and director compensation.



Northern Tier Energy LLC and its subsidiaries have historically not been subject to federal income and certain state income taxes. After consummation
of our initial public offering, Northern Tier Retail

Holdings LLC, the subsidiary of Northern Tier Energy LLC through which we conduct our retail business, and Northern Tier Energy Holdings LLC elected to be treated as corporations for federal
income tax purposes, subjecting these subsidiaries to corporate-level tax. As a result of the elections by Northern Tier Retail Holdings LLC and Northern Tier Energy Holdings LLC to be treated as corporations for federal income tax purposes, for
periods following such elections, our financial statements will include a tax provision on income attributable to these subsidiaries. Giving effect to such elections, we recorded a tax provision of $7.8 million for the nine months ended
September 30, 2012, including an $8.0 million tax charge to recognize the net deferred tax asset and liability position as of the date of the elections. On a pro forma basis after giving effect to such elections and our initial public offering,
we would have recorded a tax provision of approximately $5.7 million for the year ended December 31, 2011.



In 2010, we entered into a management services agreement with ACON Management and TPG Management pursuant to which they provided us with ongoing
management, advisory and consulting services in exchange for management fees. This management services agreement terminated in connection with the closing of our initial public offering.

2020 Notes Offering and Tender Offer

Our results of operations for periods subsequent to the completion of our 2020 Notes offering and tender offer may not be comparable to our results of operations for periods prior to the refinancing.

On November 8, 2012, we completed a private placement of $275 million in aggregate principal amount of the 2020 Notes.
We used the net proceeds of the offering and cash on hand of $31 million (i) to repurchase our outstanding 2017 Notes that were tendered pursuant to our previously announced tender offer and (ii) to satisfy and discharge any remaining 2017
Notes outstanding (which notes were called for redemption after the closing of the tender offer) and to pay related fees and expenses. The repurchase of the 2017 Notes resulted in an after-tax charge of approximately $48 million in the fourth
quarter of 2012. On a pro forma basis after giving effect to such private placement and tender offer, we would have recorded a reduction of approximately $8.9 million of interest expense for the year ended December 31, 2011. The pro forma impacts of
the private placement and tender offer and the pro forma impacts of the partial redemption of the 2017 Notes as part of our initial public offering would have resulted in a pro forma interest expense of $30.2 million for the year ended December 31,
2011.

In connection with the transactions described in the preceding paragraph, our PIK units converted into common units
representing limited partner interests with the same rights and limitations as our existing common units, effective November 9, 2012.

Major Influences on Results of Operations

Refining

Our
earnings and cash flows from our refining business segment are primarily affected by the relationship between refined product prices and the prices for crude oil and other feedstocks. Refining is primarily a margin-based business, and in order to
increase profitability, it is important for the refinery to maximize the yields of high value finished products and to minimize the costs of feedstock and operating expenses. Feedstocks are petroleum products, such as crude oil and natural gas
liquids that are processed and blended into refined products. The cost to acquire feedstocks and the price for which refined products are ultimately sold depend on several factors, many of which are beyond our control, including the supply of, and
demand for, crude oil, gasoline and other refined products, which depend on changes in domestic and foreign economies, weather conditions, domestic and foreign political affairs, production levels, availability of and access to transportation
infrastructure, the availability of imports, the marketing of competitive fuel, and the extent of government regulation, among other factors.

Feedstock and refined product prices are also affected by other factors, such as product
pipeline capacity, local market conditions and the operating levels of competing refineries. Crude oil costs and the prices of refined products have historically been subject to wide fluctuations. An expansion or upgrade of our competitors
facilities, price volatility, international political and economic developments and other factors beyond our control are likely to continue to play an important role in refining industry economics. These factors can impact, among other things, the
level of inventories in the market, resulting in price volatility and a negative impact on product margins. Moreover, the refining industry typically experiences seasonal fluctuations in demand for refined products, such as increases in the demand
for gasoline during the summer driving season and for home heating oil during the winter, primarily in the Northeast. In addition to current market conditions, there are long-term factors that may impact the demand for refined products. These
factors include mandated renewable fuels standards, proposed climate change laws and regulations, and increased mileage standards for vehicles.

In order to assess our operating performance, we compare our refinery gross product margin against an industry refining margin benchmark. The industry refining margin benchmark we use is referred to as
Group 3 3:2:1 crack spread, which is calculated by assuming that three barrels of benchmark light sweet crude oil is converted into two barrels of reformulated gasoline and one barrel of ultra low sulfur diesel. Because we calculate the benchmark
refining margin using the market value of PADD II Group 3 conventional gasoline and ultra low -sulfur diesel against the market value of NYMEX WTI, we refer to the benchmark as the Group 3 3:2:1 crack spread. The Group 3 3:2:1 crack spread is
expressed in dollars per barrel and is a proxy for the per barrel margin that a sweet crude oil refinery would earn assuming it produced and sold at PADD II Group 3 prices the benchmark production of gasoline and ultra low sulfur diesel.

Our direct operating expense structure is also important to our profitability. Major direct operating expenses include employee and
contract labor, maintenance and energy. Our predominant variable direct operating cost is energy, which is comprised primarily of fuel and other utility services. The costs of fuel, principally natural gas, and other utility services, principally
electricity, used by our refinery and other operations have historically been volatile.

Consistent, safe and reliable
operations at our refinery are key to our financial performance and results of operations. Unplanned downtime at our refinery may result in lost margin opportunity, increased maintenance expense and a temporary increase in working capital investment
and related inventory position. We seek to mitigate the financial impact of planned downtime, such as major turnaround maintenance, through a diligent planning process that takes into account the margin environment, the availability of resources to
perform needed maintenance, contractual commitments, feedstock logistics and other factors. Periodically, we have planned maintenance turnarounds at our refinery, which are expensed as incurred. The refinery generally undergoes a major facility
turnaround every five to six years, and the last full plant turnaround was completed in 2007. The length of the turnaround is contingent upon the scope of work to be completed. A major turnaround of either of the two main refinery units (fluid
catalytic cracking unit and alkylation unit) generally takes two to four weeks to complete, and is planned and accomplished in a manner that allows for reduced production during maintenance instead of a complete shutdown. We completed a partial
turnaround in April 2011, principally to replace a catalyst in the distillate and gas oil hydrotreaters, and to conduct basic maintenance on the No. 1 crude unit. At the end of March 2012, we started a planned turnaround of the alkylation unit
that was completed according to schedule in mid May 2012. The next major turnaround is scheduled for 2013.

Because petroleum
feedstocks and products are essentially commodities, we have no control over the changing market. Therefore, the lower the target inventory we are able to maintain, the lesser is the impact of commodity price volatility on our petroleum product
inventory position. Our inventory of crude oil and refined products is valued at the lower of cost or market value under the LIFO cost flow assumption. For periods in which the market price declines below our LIFO cost basis, we are subject to
significant fluctuations in the recorded value of our inventory and related cost of products sold. Since 2009, we have experienced LIFO liquidations based upon permanent decreased levels in our inventories. These LIFO liquidations resulted in
decreased cost of sales and increased income from operations of $1.7 million, $2.1 million, $2.1 million and

$4.1 million for the year ended December 31, 2009, the eleven months ended November 30, 2010, the Successor Period ended December 31, 2010 and the year ended December 31,
2011, respectively. There were no such liquidations in the nine months ended September 30, 2011 and 2012.

At the closing
of the Marathon Acquisition, we entered into a crude oil supply and logistics agreement with JPM CCC pursuant to which JPM CCC assists us in the purchase of the crude oil requirements of our refinery and provides transportation and other logistical
services for delivery of the crude oil to our storage tanks in Cottage Grove, Minnesota. In March 2012, we amended and restated the crude oil supply and logistics agreement with JPM CCC. We pay JPM CCC the price of the crude oil plus certain agreed
fees and expenses. We believe this crude oil supply and logistics agreement significantly reduces our crude inventories and allows us to take title to and price our crude oil at the refinery, as opposed to the crude oil origination point, reducing
the time we are exposed to market fluctuations before the finished product output is sold.

In addition, we may hedge a
portion of our gasoline and distillate production with the purpose of ensuring we can meet our fixed cost obligations, service our outstanding debt and other liabilities and meet our capital expenditure obligations. We have entered into agreements
that govern all cash-settled commodity transactions that we enter into with J. Aron & Company and Macquarie Bank Limited for the purpose of managing our risk with respect to the crack spread created by the purchase of crude oil for future
delivery and the sale of refined products, including gasoline, diesel, jet fuel and heating fuel, for future delivery. As market conditions permit, we have the capacity to hedge our crack spread risk with respect to a portion of the refinerys
projected monthly production of these refined products. Consistent with that policy, as of September 30, 2012, we had hedged approximately nine million barrels of future gasoline and diesel production, of which four million barrels are
related to 2012 production and the remainder to 2013 production. We intend to hedge significantly less than what we hedged at the time of the Marathon Acquisition on an ongoing basis. Consequently, we plan to increase our exposure to the gross
refining margins that we would realize at our refinery on an unhedged basis over time.

During the nine months ended
September 30, 2012, we settled contracts covering approximately three million barrels of our remaining 2012 gasoline and diesel production and recognized a loss of approximately $44.6 million. In addition, during the second quarter of 2012, we
reset the price of our contracts for the period of July 2012 through December 2012 and recognized a loss of approximately $92 million. We used $92 million of the net proceeds from our initial public offering to settle the majority of these
obligations. The remainder of these deferred losses of approximately $45 million will be paid through the end of 2013.

Our
refining business experiences seasonal effects. Demand for gasoline is generally higher during the summer months than during the winter months due to seasonal increases in highway traffic. Decreased demand during the winter months can lower gasoline
prices. As a result, our operating results of our refining business for the first and fourth calendar quarters are generally lower than those for the second and third calendar quarters of each year.

Retail

Our
earnings and cash flows from our retail business segment are primarily affected by the volumes and margins of gasoline and diesel sold, and by the sales and margins of merchandise sold at our convenience stores. Seasonal fluctuations in traffic also
affect sales of motor fuels and merchandise in our convenience stores. As a result, the operating results of our retail segment are generally lower for the first quarter of the year. Weather conditions in our operating area also have a significant
effect on our retail operating results. Customers are more likely to purchase higher profit margin items at our convenience stores, such as fast foods, fountain drinks and other beverages and more gasoline during the spring and summer months,
thereby typically generating higher revenues and gross margins for us in these periods. Margins for transportation fuel sales are equal to the sales price (which includes the motor fuel taxes) less the delivered cost of the fuel and motor fuel
taxes, and are measured on a cents per gallon basis. Fuel margins are impacted by local supply, demand and competition.

Margins for retail merchandise sold are equal to retail merchandise sales less the delivered cost of the merchandise, net of any supplier discounts and inventory shrinkage, and are measured as a
percentage of merchandise sales. Merchandise sales are impacted by convenience or location, branding and competition. Franchisees are required to pay us an initial license fee (generally, $10,000 for licensees located in Minnesota and Wisconsin and
$2,000 for licensees located in South Dakota) and a royalty fee for all products and merchandise sold at the convenience store, including motor fuel and diesel. The initial term of the license is generally 10 years, which is renewable by the
licensee for a renewal term of 10 years, subject to the licensee satisfying certain conditions. The license agreements also require that, if a franchise store is located within our distribution area, then the franchise store must purchase a high
minimum percentage (often 85% to 100%) of its motor fuel supply, including gasoline and distillate, from us. However, if a franchise store is not located within our distribution area, then the franchise store is not required to purchase any portion
of its motor fuel supply from us. As of September 30, 2012, 33 of the 68 existing franchise stores are located within our distribution area and, thus, required to purchase a high minimum percentage of their motor fuel supply from us.

Results of Operations

We operate our business in two segments: the refining segment and the retail segment. Each of these segments is organized and managed based upon the nature of the products and services they offer. Through
the refining segment, we operate the St. Paul Park, Minnesota, refinery, terminal and related assets, and through the retail segment, we operate 166 convenience stores primarily in Minnesota. The retail segment also includes the operations of
SuperMoms Bakery and SuperAmerica Franchising LLC, our wholly owned subsidiary (SAF), through which we conduct our franchising operations.

In this Results of Operations section, we first review our business on a combined and consolidated basis, and then separately review the results of operations of each of the refining segment
and the retail segment. Detailed explanations of the period over period changes in our results of operations are contained in the discussion of individual segments. For partial year periods that do not have a corresponding period of the same
duration, comparisons are made on a run rate basis comparing the partial period results with the prior years average monthly results for the corresponding period of time.

We refer to our financial statement line items in the explanation of our period over period changes in results of operations. Below are
general definitions of what those line items include and represent.

Revenue. Revenue primarily includes the
sale of refined products in our refining segment and sales of fuel and merchandise to retail consumers in our retail segment. All sales are recorded net of customer discounts and rebates and inclusive of federal and state excise taxes. Refining
revenue includes intersegment sales of refined products to the retail segment. For purposes of presenting sales on a combined basis, such intersegment transactions are eliminated. Retail revenue primarily includes sales of fuel and merchandise to
customers inclusive of related excise taxes and net of any applicable discounts. Also included in retail revenue is royalty income, revenues from car wash operations and SuperMoms Bakery sales to third parties.

Cost of sales. Refining cost of sales primarily include costs of crude and refinery feedstocks purchased, ethanol and
other refined products purchased and excise taxes paid to various government authorities. Retail cost of sales consists of cost of fuel, merchandise and other products, costs of sales for SuperMoms Bakery merchandise sales to third parties and
excise taxes paid to various government authorities. Retail cost of sales includes intersegment purchases of refined products from the refining segment. For purposes of presenting cost of sales on a combined and consolidated basis, such intersegment
transactions are eliminated.

Turnaround and related expenses. Turnaround and related expenses represent
the costs of required major maintenance projects on refinery processing units. A turnaround is a standard industry operation to refurbish and maintain a refinery and usually requires the shutdown and inspection of major processing units. Processing
units require major maintenance every five to six years.

Depreciation and amortization. Depreciation and
amortization represents an allocation to expense within the statement of operations of the carrying value of capital and intangible assets. The value is allocated based on the straight-line method over the estimated useful life of the related asset.

Selling, general and administrative. Selling, general and administrative expenses primarily include
corporate costs, administrative expenses, shared service costs and marketing expenses.

Formation
costs. Formation costs represent costs incurred in the creation of Northern Tier Energy LLC and its subsidiaries. No such costs existed for periods prior to the Marathon Acquisition.

Contingent consideration (income) expense. Contingent consideration income (expense) relates to changes in the
estimated fair value of our margin support and earn-out arrangements with Marathon. No such arrangement existed for periods prior to December 1, 2010.

Other income (expense), net. Other income (expense), net primarily represents income (expense) from our equity method investment in Minnesota Pipe Line and dividend income from our cost
method investment in Minnesota Pipe Line Company, LLC.

Gain (loss) from derivative activities. Gain (loss)
from derivative activities primarily includes impacts from our crack spread risk mitigation strategy initiated in October 2010 in anticipation of the Marathon Acquisition to mitigate market price risk. Included in gain (loss) from derivative
activities are realized gains or losses related to settled contracts during the period and unrealized gains or losses on outstanding derivatives to partially hedge the crack spread margins for our refining business. The offsetting benefits related
to these unrealized losses should be realized over future periods as improved crack spreads are realized. Going forward, we plan to hedge a lesser amount of our production than we hedged at the time of the Marathon Acquisition.

Bargain purchase gain. Bargain purchase gain represents the excess of the estimated fair value of the net assets
acquired in the Marathon Acquisition over the total purchase consideration.

Interest expense, net. Interest
expense, net subsequent to December 1, 2010 relates primarily to interest incurred on our senior secured notes as well as commitment fees and interest on the revolving credit facility and the amortization of deferred financing costs.

The historical financial data presented below are not necessarily indicative of the results
to be expected for any future period. The historical financial data for the year ended December 31, 2009 and for the eleven months ended November 30, 2010, do not reflect the consummation of the Marathon Acquisition or our capital
structure following the Marathon Acquisition. See Predecessor Carve-out Financial Statements.

Revenue. Revenue for the nine months ended September 30, 2012 was $3,417.8 million compared to
$3,192.0 million for the nine months ended September 30, 2011, an increase of 7.1%. Refining segment revenue increased 7.9% and retail segment revenue decreased 3.8% compared to the nine months ended September 30, 2011. The refining
segment benefited from higher average market prices for refined products and higher sales volumes. Retail revenue decreased primarily due to lower fuel sales volumes caused by reduced market demand and road construction projects impacting our retail
stores. Excise taxes included in revenue totaled $215.0 million and $181.5 million for the nine months ended September 30, 2012 and 2011, respectively.

Cost of sales. Cost of sales totaled $2,594.0 million for the nine months ended September 30, 2012 compared to $2,578.2 million for the nine months ended September 30, 2011, an
increase of 0.6%, due to the impact of increased refining throughput, partially offset by lower priced crude oil as a result of favorable crude differentials in the second and third quarters of 2012. Excise taxes included in cost of sales were
$215.0 million and $181.5 million for the nine months ended September 30, 2012 and 2011, respectively.

Direct
operating expenses. Direct operating expenses totaled $189.1 million for the nine months ended September 30, 2012 compared to $192.5 million for the nine months ended September 30, 2011, a decrease of

1.8%, due primarily to lower operating expenses at our retail stores and reduced utility expenses at the refinery, which were driven by lower utility rates and reduced usage due to favorable
weather conditions in the first quarter of 2012, offset by costs recognized in the 2012 period related to environmental compliance projects at our refinerys wastewater treatment plant.

Turnaround and related expenses. Turnaround and related expenses totaled $17.1 million for the nine months ended
September 30, 2012 compared to $22.5 million for the nine months ended September 30, 2011. Both periods include costs related to planned, partial turnarounds. The 2012 turnarounds include the alkylation unit, which was completed according
to schedule in mid-May, and the No. 1 reformer unit, which was completed in early November. The 2011 turnaround was principally to replace catalyst in the distillate and gas oil hydrotreaters and to conduct basic maintenance on the No. 1
crude unit.

Depreciation and amortization. Depreciation and amortization was $24.6 million for the nine
months ended September 30, 2012 compared to $22.3 million for the nine months ended September 30, 2011, an increase of 10.3%. This increase was primarily due to depreciation of assets placed in service since September 30, 2011
primarily related to our refinery and our systems implementation project.

Selling, general and administrative
expenses. Selling, general and administrative expenses were $67.1 million for the nine months ended September 30, 2012 compared to $63.3 million for the nine months ended September 30, 2011. This increase of 6.0% from
the prior year period relates primarily to higher administrative costs incurred during the first six months of 2012 related to post go-live systems support during the process optimization phase of our standalone systems implementation and higher
compensation costs and risk management expenses in the 2012 period.

Formation costs. Formation costs for
the nine months ended September 30, 2012 and 2011 were $1.0 million and $6.1 million, respectively. The formation costs in the 2012 period relate to offering costs for our initial public offering that did not meet the accounting
requirements for deferral. This second quarter 2012 charge was incurred by Northern Tier Energy LP but was not an expense of Northern Tier Energy LLC. All of the costs from the 2011 period are attributable to the Marathon Acquisition.

Contingent consideration loss (income). Contingent consideration loss was $104.3 million for the nine months ended
September 30, 2012 compared to contingent consideration income of $37.6 million for the nine months ended September 30, 2011. The contingent consideration losses relate to the margin support and earn-out agreements entered into with
Marathon at acquisition. The 2012 charge of $104.3 million includes the impact of the final valuation adjustment to arrive at the agreed settlement amount which was contingent upon our initial public offering. The contingent consideration income in
the 2011 period relates to changes in the financial performance estimates as of September 30, 2011 for the then remaining period of performance.

Other income, net. Other income, net was $6.2 million for the nine months ended September 30, 2012 compared to $2.4 million for the nine months ended September 30, 2011. This
change is driven primarily by increases in equity income from our investment in Minnesota Pipe Line Company, LLC.

Gains
(losses) from derivative activities. For the nine months ended September 30, 2012, we had realized losses of $165.0 million related to settled contracts compared to $246.4 million in the prior-year period. Offsetting benefits
related to these losses were recognized through improved operating margins. We incurred unrealized gains on outstanding derivatives of $32.6 million for the nine months ended September 30, 2012 compared to unrealized losses of $334.5 million
during the nine months ended September 30, 2011. These derivatives were entered into to partially hedge the crack spreads for our refining business. In addition to these impacts, during the nine months ended September 30, 2012, we entered
into arrangements to settle or re-price a portion of our existing derivative instruments ahead of their respective expiration dates and incurred $136.8 million of realized losses related to these early extinguishments. We settled $92 million of
this early extinguishment obligation out of the net proceeds of our initial public offering.

Interest expense, net. Interest expense, net was $36.7 million for the
nine months ended September 30, 2012 and $30.6 million for the nine months ended September 30, 2011. These interest charges relate primarily to the 2017 Notes as well as commitment fees and interest on the ABL facility and the amortization
of deferred financing costs. The increase from the prior-year period is primarily due to the write-off of $4.6 million of deferred financing costs caused by the partial redemption of the 2017 Notes and the refinancing of our ABL facility.
Additionally, the 2012 period includes approximately $0.9 million of incremental interest charges related to the 3% premium paid upon the partial redemption of the 2017 Notes.

Income tax provision. The income tax provision for the nine months ended September 30, 2012 was $7.8 million compared to less than $0.1 million for the nine months ended
September 30, 2011. Prior to July 31, 2012, we operated as a pass-through entity for federal tax purposes and, as such, only state taxes were recognized. Effective on July 31, 2012 our retail business became a tax paying entity for
federal and state income taxes. The charge in the third quarter of 2012, relates primarily to the recognition of an $8.0 million net deferred tax liability on the effective date of the conversion of our retail business to a tax paying entity.

Net income (loss). Our net income was $113.1 million for the nine months ended September 30, 2012
compared to a net loss of $264.4 million for the nine months ended September 30, 2011. This improvement of $377.5 million was primarily attributable to a $233.6 million increase in operating income for our refining segment due to refining gross
margins in the second and third quarters of 2012 and a reduction in losses related to derivative activities of $311.7 million. These improvements were partially offset by a $141.9 million unfavorable impact in contingent consideration adjustments.

Year Ended December 31, 2011 (Successor) Compared to the Eleven Months Ended November 30, 2010 (Predecessor)

Revenue. Revenue for the year ended December 31, 2011 was $4,280.8 million compared to $3,195.2
million for the eleven months ended November 30, 2010, an increase of 22.8% from the average monthly run rate for the 2010 period. Refining segment revenue increased 24.5% and retail segment revenue increased 7.3% compared to the average
monthly run rate for the eleven months ended November 30, 2010. The refining segment benefited from higher average prices across our principal products driven primarily by increased market prices for refined products. Retail revenue also
benefited from higher average fuel prices that were partially offset by lower sales volumes and lower merchandise sales. Excise taxes included in revenue totaled $242.9 million and $271.8 million for the year ended December 31, 2011 and the
eleven months ended November 30, 2010, respectively.

Cost of sales. Cost of sales totaled $3,508.0
million for the year ended December 31, 2011 compared to $2,697.9 million for the eleven months ended November 30, 2010, an increase of 19.2% from the average monthly run rate for the 2010 period, due primarily to higher priced crude oil
and other feedstock costs. Cost of sales as a percentage of revenue decreased from 84.4% for the eleven months ended November 30, 2010 to 81.9% for the year ended December 31, 2011 due to the increased revenues resulting from higher
refined product average prices. Excise taxes included in cost of sales were $242.9 million and $271.8 million for the year ended December 31, 2011 and the eleven months ended November 30, 2010, respectively.

Direct operating expenses. Direct operating expenses totaled $260.3 million for the year ended December 31, 2011
compared to $227.0 million for the eleven months ended November 30, 2010, an increase of 5.1% from the average monthly run rate for the 2010 period, due to higher rent costs in our retail segment as a result of the sale-leaseback arrangement
entered into in connection with the Marathon Acquisition and higher credit card processing fees in our retail segment as a result of the higher revenues.

Turnaround and related expenses. Turnaround and related expenses totaled $22.6 million for the year ended December 31, 2011 compared to $9.5 million for the eleven months ended
November 30, 2010. The increase from the 2010 period is primarily due to the timing and scope of the scheduled turnaround projects undertaken in the

respective periods. The 2011 period included a scheduled partial turnaround at the refinery in April principally to replace a catalyst in the distillate and gas oil hydrotreaters and to conduct
basic maintenance on the No. 1 crude unit.

Depreciation and amortization. Depreciation and
amortization was $29.5 million for the year ended December 31, 2011 compared to $37.3 million for the eleven months ended November 30, 2010, a decrease of 27.5% from the average monthly run rate for the 2010 period. As part of the Marathon
Acquisition, the real estate for the majority of our convenience stores was sold and as a result we are no longer depreciating these convenience store buildings. Additionally, as a result of purchase accounting, the book value of our refinery was
increased and its estimated useful life was extended. The impact of these purchase accounting adjustments is a net decrease in overall refinery depreciation.

Selling, general and administrative expenses. Selling, general and administrative expenses were $90.7 million for the year ended December 31, 2011 compared to $59.6 million for
the eleven months ended November 30, 2010. This increase of 39.5% from the average monthly run rate for the 2010 period reflects higher administrative costs as we developed our standalone infrastructure throughout the year while continuing to
pay transition services fees of $21.1 million in 2011 to utilize Marathon systems. As a result, there was a period of overlap and redundant cost structures during this infrastructure development.

Formation costs. Formation costs for the year ended December 31, 2011 were $7.4 million, all attributable to the
Marathon Acquisition. We did not incur any such costs in the eleven months ended November 30, 2010.

Contingent
consideration income. Contingent consideration income was $55.8 million for the year ended December 31, 2011, which is due to updated financial performance estimates for the period of performance under the margin support and
earn-out provisions included in the Marathon Acquisition agreements.

Other income, net. Other income, net
was $4.5 million for the year ended December 31, 2011 compared to $5.4 million for the eleven months ended November 30, 2010. This change is driven primarily by changes in equity income from our investment in the Minnesota Pipe Line
Company.

Loss from derivative activities. For the year ended December 31, 2011, we had realized losses
of $310.3 million related to settled contracts. Offsetting benefits related to these losses were recognized through improved operating margins. We incurred unrealized losses of $41.9 million for the year ended December 31, 2011 on
outstanding derivatives entered into to partially hedge the crack spread margins for our refining business through 2012. We incurred unrealized losses on these outstanding derivatives of $40.9 million for the eleven months ended November 30,
2010. The offsetting benefits related to these unrealized losses should be realized over future periods as improved operating margins are realized.

Interest expense, net. Interest expense, net was $42.1 million for the year ended December 31, 2011 compared to $0.3 million for the eleven months ended November 30, 2010. This
increase was primarily attributable to the issuance of the 2017 Notes as well as commitment fees and interest on our revolving credit facility and the amortization of deferred financing costs.

Income tax provision. Income tax expense was less than $0.1 million for the year ended December 31, 2011 compared
to $67.1 million for the eleven months ended November 30, 2010. The effective tax rate was 52.4% for the eleven months ended November 30, 2010. The effective rate was impacted primarily by the establishment of a valuation allowance against
capital losses incurred on derivative activities. The effective tax rate is not comparable to the year ended December 31, 2011. From the date of the Marathon Acquisition, only state taxes have been recognized and no federal provision was
recognized. We operated as a pass-through entity for federal income tax purposes for the year ended December 31, 2011.

Net earnings. Our net earnings were $28.3 million for the year ended December 31, 2011 compared to net earnings of
$61.0 million for the eleven months ended November 30, 2010. This decrease of 57.5% from the

average monthly run rate for the 2010 period was primarily attributable to the realized loss on derivative activities of $310.3 million and an increase in interest expense, partially offset by
increased operating income and lower income taxes.

2010 Successor Period from June 23, 2010 (inception date) through
December 31, 2010

Northern Tier Energy LLC was formed on June 23, 2010 and entered into certain agreements
with Marathon on October 6, 2010 to acquire the Marathon Assets. At the closing of the Marathon Acquisition on December 1, 2010, Northern Tier Energy LLC acquired the Marathon Assets. Northern Tier Energy LLC had no operating activities
between its June 23, 2010 inception date and the closing date of the Marathon Acquisition, although it incurred various transaction and formation costs which have been included in the 2010 Successor Period.

The discussion below presents a comparison of the 2010 Successor Period and 2009 monthly average run rates, and does not seek to compare
the 2010 Successor Period to the equivalent period in the prior year.

Revenue for the 2010 Successor Period was $344.9
million. Revenue for the 2010 Successor Period was favorably impacted by price increases across both the refining and retail segments. Refining and retail segment revenues increased 48.1% and 9.4% compared to 2009 average monthly run rate revenues.
Cost of sales for the 2010 Successor Period was $307.5 million. Excise taxes included in both revenue and cost of sales were $25.1 million for the 2010 Successor Period. Cost of sales as a percentage of revenue was 89.2% for the 2010 Successor
Period compared to 85.3% for 2009.

The 2010 Successor Period included two significant non-recurring items: formation costs of
$3.6 million and a bargain purchase gain of $51.4 million, both related to the Marathon Acquisition. Additionally, during the 2010 Successor Period, we incurred unrealized losses of $27.1 million on outstanding derivatives entered into in 2010 to
partially hedge the crack spread margins for our refining business for 2011 through 2012. The offsetting benefits related to these unrealized losses will be realized over future periods as the improved crack spread margins are realized.

Our net earnings were $24.8 million for the 2010 Successor Period, compared to 2009 average monthly run rate net earnings of $4.6
million. The net earnings in the 2010 Successor Period include $3.6 million of formation costs, $27.1 million of unrealized derivative losses and a $51.4 million bargain purchase gain, all of which were related to the Marathon Acquisition and did
not occur in the 2009 period.

Eleven Months Ended November 30, 2010 Compared to Year Ended December 31, 2009

Revenue. Revenue for the eleven months ended November 30, 2010 was $3,195.2 million compared to
$2,940.5 million for the year ended December 31, 2009, an 18.5% increase versus the average monthly run rate for 2009. Refining and retail segment revenue increased to $2,799.8 million and $1,206.8 million, respectively, which represent
increases of 20.7% and 16.6%, respectively, versus the 2009 average monthly run rate levels. These increases were primarily due to increases in the market prices for refined products across the periods. Federal and state excise taxes included in
revenue totaled $271.8 million and $289.6 million for the eleven months ended November 30, 2010 and year ended December 31, 2009, respectively.

Cost of sales. Cost of sales for the eleven months ended November 30, 2010 was $2,697.9 million compared to $2,507.9 million for the year ended December 31, 2009, a 17.3%
increase versus the average monthly run rate for 2009. This increase is primarily due to increased market prices for crude oil in the 2010 period. Cost of sales as a percentage of revenue was 84.4% and 85.3% for the eleven months ended
November 30, 2010 and year ended December 31, 2009, respectively. Excise taxes included in cost of sales were $271.8 million and $289.6 million for the eleven months ended November 30, 2010 and year ended December 31, 2009,
respectively.

Direct operating expenses. Direct operating expenses for the eleven months ended
November 30, 2010 were $227.0 million compared to $238.3 million for the year ended December 31, 2009, a 3.9% increase versus

the 2009 average monthly run rate. The increase was primarily due to higher utility costs in the refining segment and higher credit card fees in the retail segment.

Turnaround and related expenses. Turnaround and related expenses totaled $9.5 million for the eleven months ended
November 30, 2010 compared to $0.6 million for the year ended December 31, 2009. This increase is primarily due to a scheduled partial turnaround at the refinery during September and October 2010.

Depreciation and amortization. Depreciation and amortization was $37.3 million for the eleven months ended
November 30, 2010 and $40.2 million for the year ended December 31, 2009, a 1.2% increase versus the 2009 average monthly run rate. The increase versus the prior year relates primarily to the on-going investment in our refinery
infrastructure.

Selling, general and administrative expenses. Selling, general and administrative expenses
for the eleven months ended November 30, 2010 were $59.6 million compared to $64.7 million for the year ended December 31, 2009, a 0.5% increase versus the 2009 average monthly run rate.

Other income, net. Other income, net was $5.4 million for the eleven months ended November 30, 2010 compared to
other income, net of $1.1 million for the year ended December 31, 2009. This improvement is due to higher equity income from our investment in the Minnesota Pipe Line Company.

Loss from derivative activities. We incurred unrealized losses of $40.9 million for the eleven months ended
November 30, 2010 on outstanding derivatives entered into during 2010. The offsetting benefits relating to these unrealized losses should be realized over future periods as improved operating margins are realized. No such derivative activity
existed for the year ended December 31, 2009.

Interest expense, net. Interest expense, net was $0.3
million for the eleven months ended November 30, 2010 and $0.4 million for the year ended December 31, 2009.

Income tax provision. Income tax expense was $67.1 million for the eleven months ended November 30, 2010 and $34.8
million for the year ended December 31, 2009. The effective tax rate was 52.4% for the eleven months ended November 30, 2010 and 38.9% for the year ended December 31, 2009. The effective rate for the eleven months ended
November 30, 2010 was impacted primarily by the establishment of a valuation allowance against capital losses incurred on derivative activities.

Net earnings. Our net earnings were $61.0 million for the eleven months ended November 30, 2010 and $54.7 million for the year ended December 31, 2009. The increase in net
earnings is primarily due to the improved gross product margin in our refining business in the 2010 period. Refinery gross product margin per barrel of throughput were $12.86 for the eleven months ended November 30, 2010 and $9.36 for the year
ended December 31, 2009.

The segment financial data for the refining segment discussed below under Refining Segment include intersegment sales of
refined products to the retail segment. Similarly, the segment financial data for the retail segment discussed below under Retail Segment contain intersegment purchases of refined products from the refining segment. For purposes of
presenting our combined and consolidated results, such intersegment transactions are eliminated, as shown in the following tables.